Terra Nova/WMG

Terra Nova actually isn’t in an alternate timeline, it really is in the past.
Eventually they will do something that affects the time stream. The secret is that they have enough time to develop technology and get off the planet before affecting anything major.
 * I mean, they practically yelled "THIS IS THE SAME TIMELINE" in your face in Episode 1 when they explained that their method of checking if it wasn't the same timeline was by sending a Sputnik-sized probe through and hoping to find it somewhere on Earth several million years later...as opposed to a sensible plan, like, sending through a rocket that would embed itself in the surface of the Moon.

Terra Nova takes place in the James Cameron created Avatar/Aliens universe
I know EVERY fan of this show insists this is not Avatar with dinosaurs but C'MON, the Space/Time Travel Marines carry the same weapons and (mostly) the same gear as their motion picture counterparts. Use a small amount of the same military jargon, HELL the SAME Colonel Badass from Avatar is in this Frickin thing.

The only plausible explanation would or could be is this that most likely that this takes place somewhere from James Cameron's Avatar/Aliens universe. Basically the whole backstory could go like this. the Wayland-Utani Corporation wasted enough money just trying to collect the Xenomorph alien species and enough Unobtainium for a useable military fleet in just a few decades this ruined the Earths economy. Thus because of this global financial downfall rampant corruption and greed became not just a part of daily life but a necessary part just for basic survival (if one doesn't ask for bribes and kick backs either they or their families could starve).

Fortunately enough Wayland-Utani found a way to invent a portal to an alternate past universe where dinosaurs exist and fresh new supplies and resources could be found for Humanities survival, so they send a group of colonists (scientists, soldiers, machine experts..etc.) through the portal to start a new life in this new world and possibly bring back some of these found resources to the Crapsack old earth. But (if any of the latest Terra Nova previews could be believed) Wayland-Utani is still up to its old tricks because Terra Nova has some unique alien species, fuel element, magnetic phenomenon, exotic what have you that the Company 'Must have all costs.

if anyone has any more opinions on this WMG Theory feel free to comment or add.
 * The state of the Earth's environment in the pilot and the comments about it in Avatar are pretty similar. Could be that Pandora exists in the Terra Nova verse and it just hasn't been mentioned yet.

Shannon is the grandson (Great-grandson? Great-great-grandson?) of Jack Carter.
His behavior and mannerisms are very similar to Jack's, and if you weren't watching the screen and only heard his voice, you'd swear it was the same man. Jim grew up hearing stories about Jack's adventures in a sweet little town where the future began, back in the days before it all went bad, and went into law enforcement in honor of his ancestor.
 * His relationship with Josh is also fairly reminiscent of Jack's relationship with Zoe at the beginning of Eureka.
 * Sure, Maddy gets some of her smarts from her mother, but quite a bit of it comes from Zoe's genes.

There will be troodontid dinosauroids
And they will obviously be humanoid and scaly to be as out-dated as humanely possible.
 * So we should "Watch Out For Sleestacks?"

Terra Nova is really in the past on a doomed continent.
They are on a continent which we have no record of - it was far out in the ocean and eventually sank under the continental plates and was eventually subducted. No trace ever remained for the future, that’s why no one ever found the probe. Otherwise they would be able to say “We’re in the vicinity of what will eventually be [place name]”.
 * Let's see, a group of people with highly advanced technology living on a continent that is unheard of in the future. Can we just all it Atlantis already?

Terra Nova actually isn’t in an alternate timeline, it’s in the far future.
The messages on the rocks are from the “future” they left - after all Nate‘s son went missing “long ago“ and seems to be responsible for the marks at the falls. The sixers suspect this is the reason no one ever found the probe.
 * If the Sixers suspect this, why did they say "control the past, control the future"? I still think this is a sound theory, but the Sixers we've seen thus far do not seem to have a clue.
 * Or they were talking about a different past. Several people mention that the Sixers have someone in the 'future'. Maybe they know more than the colonists.

Remember Kara, the girlfriend Josh left behind in 2149? She will win the lottery and come to Terra Nova.
Seriously, do you think that the show would show her if she wasn't going to affect Josh's relationship with Skye later on? Kara would be a perfect Chekhov's Gunman, not to mention trigger a Love Triangle.

The Sixers are from Terra Nova's future.
Terra Nova may not be part of Earth Prime's time-stream, but its got to be part of SOMEBODY'S time-stream. And the people from Future! Terra Nova must be mighty PO'd about these hostile temporal invaders trying to stomp all over their prehistoric butterflies.
 * That depends on what kind of temporal system the show is using. If we assume a stable time loop, everything being done is already part of that universe's time-stream. The Sixers could still have come from the future, but they are correcting whatever the secret plan is.

Terra Nova isn't a parallel earth at all. It's a completely separate planet that happens to have dinosaurs in 2149.
The odd symbols on the rocks bear a resemblance to some crop circle designs. It could end up that it's an alien language and/or a map detailing the planet's place in the galaxy.
 * Don't forget that the stars are wrong. Oh, sure, there's 85 million years of stellar drift to account for...or they're on the wrong planet.
 * The other planets and moons should still be the same if they were on Earth. You would've think somebody would noticed that Mars was missing.
 * Who said they didn't? The commander has shown himself willing to keep secrets when necessary, and 85 million years of stellar drift would confuse modern astronomers enough that casual observers wouldn't be able to figure it out.

Skye is The Mole for The Sixers

 * I support this WMG.

Terra Nova is actually Kobol.

 * This theory I endorse!

Washington has a crush on Taylor.

 * This might just be admiration for her commanding officer, but she's very close to Taylor.

There is another colony somewhere in this world

 * Where Walter Bishop is creating the machines of the First People.

The colonists are Genre Blind and its all our fault.
Teenagers being teenagers aside, lets look at the first episode. They went through a hole in the fence, into dinosaur-infested wildness. They find weird markings, but have made no apparent attempts to decipher them. They're brewing alcohol from... things, and then when they get attacked by dinosaurs they start invoking It's Quiet... Too Quiet. At no point do they point out "hey, we have batteries, this is a vehicle, why not drive away?"

Hypothesis: between now and 2149, as a result of the existence of TV Tropes, popular fiction is going to stop doing remakes and start using really out-there ideas. This trend will get more and more pronounced, until the day came when the fiction got totally divorced from reality. And now, when they most need the mental toolkit to survive a disaster movie, these poor sods have no idea what to do next.

The Sixers are the good guys.
Commander Taylor behaves more and more like a dictator. And the Sixers' opposition seems to be directed more against him as a person and not against the Terra Nova project as such. It might turn out that they're at least partially justified.
 * Alternatively, this is an attempt at cultivating a Good Prince/Benevolent Dictator Pericles type figure gone, as is par for the course in this show, horribly wrong. Note that the Liberal Democracy as we know it is a very modern invention. There's nothing that says another century and a half of societal shift, especially given the conditions we saw, might not shift cultural expectations towards another form of government. It's also worth noting that once Pericles died without leaving a successor, the Athenian direct democracy came close to tearing the city-state apart. And by all appearances Mira controls the Sixers with just as authoritative a fist.

Lucas Taylor is the scientist that discovered the portal.
He does seem to know alot about how it works to the point where he s able to provide the Sixers  Maybe part of the reason why he has such an ax to grind against his father is because he is the one who has gotten most of the fame for something that was the result of Lucas's research. This leads too..

Washington is the Sixers Mole
She's the person that Commander Taylor trusts most. The information she gets is stuff she would know. At the end of VS, she doesn't seem happy that Jim is cleared. It also sets up Mentor vs Student once again as well.

Commander Taylor is a SEAL
Because Commander is a Navy Rank

== The reason the future sucks is... ==

Mira and the Sixers will eventually pull a Heel Face Turn
forcing them to team up with the colony in order to survive.

Terra Nova is not the past of a parallel Earth, it is purgatory
The portal is not sending people to a parallel Earth, it is vaporizing them in a plasma field so intense it doesn't give anyone a chance to scream. This is done as a means of population control. The winners of the lottery are actually the losers. They start off by sending fairly legitimate people through to throw everyone off, but will eventually start emptying prisons and poor neighborhoods. They'll claim it's to put the prisoners in a more secure facility on Terra Nova and to give the poor and degenerate a chance to reform and have better lives.

Lost Did It

Alternatively there's a fringe group that believes this is what's happening (even though it's not) since no one ever comes back from Terra Nova. They intend to destroy the portal which they think is simply a tool of mass genocide.

Season 2 (dear God, please let there be a season 2) will involve the invasion of Terra Nova.
Even if Lucas manages to make the portal go both ways, his backers can't just start strip-mining prehistoric Earth while Terra Nova is still around. It's easy to see Taylor declaring Terra Nova a sovereign nation and raising an army to fend off invaders coming through the portals.

2149 Skye Tate is descended from 2025 Sky Tate.
I refuse to believe it's a simple case of Name's the Same.

Mira's daughter is already dead.
She herself said the job was only supposed to take a few months. A few years later, Taylor's still alive and the portal's still one-way. The Sixers' backers probably decided the Sixers had failed and liquidated the hostages they were using as leverage. Of course, when the Sixers established communications with the future this fact was kept from them, with all requests for communication with their loved ones refused with a "You can talk to them once Taylor is terminated." or somesuch line.

They aren't in the past.
The wooden figurehead that appeared at the end of the Season Finale has the potential to explain all of the history breaks that the show has caused. My friend came up with the theorem that, perhaps they're not in the past, but -very far into the future-, which would explain unseen dinosaurs, why the moon is ridiculously close, why the continents are wrong (They could be re-aligning differently.) why some dinosaurs are evolved differently, etc.. Because, who would think it's a great idea to bring a random 18th century wooden boat figurehead into the future? Not I. The only explanation I can come up with is that something in the 18th century secretly discovered time travel, which is completely implausible. But hey, it's just a theory, and there's likely holes.

Boylan is actually a Knight in Sour Armor who is ultimately loyal to Taylor. In fact, he use to be one of Taylor's most loyal officers.
We know several things about Boylan and his relationship with Taylor. First, they served together. Second, they use to be good friends. Third, Boylan caught Taylor in the aftermath of the General's murder at Taylor's hand. Fourth, Taylor bribed Boylan to both not report the death (and turn Taylor in, effectively) as well as bury the body and keep everything a secret. Given other signs within the show about the relationship Taylor cultivates with his men (especially those loyal to him), scenes involving Boylan (Boylan being the one to shoot the Sixer in the infirmary, Boylan helping with the murderer), and so forth, it seems as if, from Boylan's perspective this is what happened: he, like the others, idolized and respected Taylor tremendously. However, when he sees his mentor and do-no-evil leader do something ignoble and force him to do the same, his faith in the idea of a Big Good is shattered - that everyone then must have some evil or ignoble part of them. He simply can not fully mesh the Big Good image of Taylor with the first hand experience of the coverup. And so Boylan becomes very cynical over the years and such. Taylor for his part comes to view Boylan as 'weak' and 'cowardly' and not so much evil for Boylan's situation; for Taylor, things are pretty much black and white and pretty straight forward. So for Taylor, he dislikes Boylan's percieved lack of mental fortitude and ability to cope. However, he allows Boylan's little den of gambling out of loyalty and perhaps out of a little guilt over the matter; Boylan's bar and Boylan himself (especially when he called out Taylor that his was the only place people could get away) are a uncomfortable reminder to Taylor (as we know Taylor isn't exactly one to deal with uncomfortable social situations too well). All this is also how Boylan can reconcile his dealings with the Sixers - if his idol Taylor can do a little bad deed that doesn't get anyone hurt, why can't he? After all, Boylan was only trading for supplies really - something he could justify as harmless.

Terra Nova isn't when (and possibly where) they think it is
The reason there are dinosaurs running around is the same reason that there's a figurehead in the Badlands and humans and 2149 technology at the colony - because they all came through various portals. The dinosaurs possibly arrived first, thrived there, and set up a large ecosystem that resembles the Cretaceous, but is wrong in a lot of the details (as seen in the Somewhere a Palaeontologist Is Crying on the Trivia page) because the plants and animals actually came from different times.

Possibly locations are the far future, an alternate Earth that didn't evolve life (or that life was superseded by the "alien" life from the portals), or another planet altogether (less likely, since that moon sure looks like ours, despite being larger).