Megas XLR/WMG

Megas was meant to be sent back to 1936
Megas was never designed to turn the tables of the war with the Glorft through direct combat. Instead, it was sent back to try and advance human technology to the point that, by the time they were at war with the Glorft, Earth would be technologically superior. However, the plan was never told to Kiva (all she was told was that she was being sent back to a "pivotal point in the war", and gambled that she could adapt) because she was willing to sacrifice herself to the cause, plus she had knowledge of the technology in Megas, thus aiding the assimilation of Megas' technology into 1936.
 * However, no one could have foreseen Megas falling into the hands of Coop, who kept Megas's tech to himself.
 * Also, they never said that the turning point in the "War" was the war between humanity and the Glorft. They could have meant WWII, for some reason.

Evil Coop from Rearview Mirror, Mirror somehow managed to make himself part of the Dai-Gurren Brigade.
Look at the icon behind his chair. Doesn't it look an awful lot like the top half of the Dai-Gurren Brigade symbol?
 * Megas runs on Spiral Energy of course, but everyone already knows that.
 * How else did merging with the s-force mecha By smashing MEGAS's limbs into them work?
 * Makes sense, the only way possible to stop the Dai Gurren Brigade was through Megas so they sent in Evil Coop in an attempt to sabotage their efforts, promising him membership. Obviously it didn't work that way so they were forced to erase the entire MEGAS XLR universe off the map.
 * The show wasn't out by that time. Evil Coop is clearly a parody of Char and his various incarnations in the Gundam universe.
 * Or perhaps Dai Gurren is duplicating evil!Coop's awesome taste.
 * Kamina's father is descended either from Evil!Coop or someone who found a journal, which include the symbol, of tales about the good ol' days of Megas without the evil empire. The spiral armies that develop after the first Anti-Spiral onslaught were reverse engineered Megas units. Gurren was just the tech minimized to work with dang near anything.

Evil Coop is Kamina's father
Just to hook with the theory above. And yeah, he probably gave all that noble speech to Shota Kamina before turning evil (and finished destroying the surface, blah blah blah). Yoko is Kiva's daughter, and Simon is probably Jamie's. Leeron's dad was Goat. Don't imagine how.

If the series continued, there would be a story arc of Coop, Jamie, and Kiva going into the future, and facing the Glorft once and for all.
And that would be the series finale.

Coop is a Technopath
This explains how he is the only one able to pilot Megas despite its nonsensical controls, and why the buttons seem to be able to do just the right thing no matter which one he presses. It also explains why Megas imitates his movements (dusting his hands off, leaning on a structure while thinking)

Alternatively, Megas has telepathic controls.
Both Kiva and Coop just used their own understanding of technology and Megas acts accordingly. Kiva refuses to accept Coop's "neanderthal technology" so she can't synch. Coop himself just doesn't think about the contradictions like the Context Sensitive Button; so he's able to do far more with it.

Kiva is Scottish and has an dara sealladh
An dara sealladh refers to the ability to see the future, typically a person's death, in a symbolic way. In other words, Kiva is psychic and can see through time. But by the time Kiva is born, that power extends to controlling time. Kiva, being young, is unaware of her full potential, and was meant to have a few more years of training before attempting a time jump, but was pushed through the commander track at a young age because if something went wrong, she could save herself for another attempt. It would also explain how she followed MEGAS before the tracking system was turned on and without a navigational system.

Had the show continued, they would have eventually parodied Neon Genesis Evangelion.
Because it's pretty much the only show they didn't get around to. It probably would have involved, say, Coop trying to teach a Shinji Captain Ersatz and inevitably scarring him in the process, and a Gendo Captain Ersatz trying to romance the Unit-01 stand-in.
 * And don't forget they'd parody Gurren Lagann. I bet the Kamina Captain Ersatz would become BFF with Coop.
 * Either that or he'd tell the Hot-Blooded characters to "chill out" repeatedly, eventually them taking the advice and dooming the local humans like he did with the S-Force.
 * Megas with Lagann for a head... can the universe take it???
 * Or better yet, he merges it with a Space Colony, turning it into an even bigger Megas that's temporary.
 * Alternatively Coop just unplugs the Eva equivalents from from their wall sockets and walks away.
 * Coop causes Third Impact and chugs Gendo.
 * And thus becomes Evil Coop!
 * Thats all pretty likely and NGE was considered one of CartoonNetworks most popular Humongous Mecha series (next to Mobile Suit Gundam Wing) and this was only after one initial daytime airing and it was just the pilot episode!. Ones theorizing/fantasizing could go even further. Jamie's uncontrollable drooling/lecherizing over the Rei/Suzuka Expys and their version of Plug Suits, Coop's Crowning Moment of Awesome by tearing apart a Angel before any of the Evas even twitch a finger (or in a Continuity Nod to the series 1st ep Coop destroys the other EVA units to make the fight between him and the Angel more "fair".). And to top it all off the Gendo Ersatz's comically overly complicated explanation of his version of Instrumentality which culminates in turning everyone not into orange soda but 3-flavored Mega-Slush as to which Coop only responds with a Flat What.
 * Fortunately most of Cartoon Networks more popular series are always given the opportunity to return at any time the shows creators have free to them. And as a possible CMOA for the series as a whole the Megas/NGE crossover ep may be made either as a 2 hour long special and/or as a special direct to DVD boxset which would give enough airtime to show as much parodying of Evangelion and even Gainax Studios as possible. Who knows maybe even a few characters from FLCL might just show up for fun (although admittedly a fight scene with Coop, Megas, and the alien girl with a electric guitar (her name escapes me right now) against an entire army of Angels would be the very definition of Crazy Awesome!!).
 * End of Megas anyone?
 * Coop is the main character, with Kiva as the Asuka equivalent. Our choices are Giant naked Jamie or Giant naked Goat...we can always go further back and involve other angels such as Kaworu, which has the human features and relatability to the lead, what's the closest we have to Coop in anime proper? Probably Kamina. Plus there's the duct taped photonic stabliser to think about. So Kamina swoops down and stops Megas going nuclear (Equivalent to 3rd impact since a similiar system overload destroyed a massive junk planet) by impaling the mech with a giant drill. It all fits togeather like furious oil-stained stickle-brix. As for the end of Megas, screw that, we're dealing with a ressurrection here. We go the rebuild route. 3 movies parallel to rebuild proper, including the climax of 2.22, the berserk ascencion.

Tsuruya-san had some part in the creation of this universe.
Haruhi decided to make a universe with mecha, and decided to give Tsuruya control of this universe. To supervise, Haruhi sent an avatar of herself in the form of Kiva.
 * That explains the name "Megas".

Metalocalypse and Megas XLR take place in the same universe.
The common element? Goat. One of Coop's friends, and based on the first episode of Metalocalypse, a big Dethklok fan. Since he lost his eye at a concert, it's safe to presume Megas XLR came first timeline-wise.
 * That would put both in the same universe as Downtown-the show Goat (not his real name) started in.
 * That explains why so much of Megas uses '80s-tech.

Magnanimous actually is Bruce Campbell
He was somehow hyper-evolved by AIM at some point in the future, then went back in time to host robot fights for his own amusement.

The REGIS Mrk.5 from episode 3 was a Necron.
Black Robot, trying to wipe out all life on the planet, hard to Kill, sounds like a Necron to me.
 * It could also be a Berserker.
 * It's a Sentinel from The Matrix, dropped back through time.
 * It's a Terminator prototype, ditto.
 * It's Omnius. He was popped into another universe at the end of the Brian Herbert/Kevin Anderson series. The Megas-verse was where he ended up.
 * It's one of the Omega WEAPON Prototypes! The bestiary DID say the previous 11 wound up in some damn odd places, and we've only got about 8 or so accounted for....

It was planned to give to Kiva and jamie they own mecha's, if it continued
Well, it never mentioned what happened to the robots Kiva take from the future in the first episode.
 * Didn't Coop destroy them to make the battle with the Glorft fair?
 * He knocked it over and made it useless...but it probably got destroyed anyways...
 * I believe the UMD fell on top of it. The children cheered. Jerks. That was an awesome mech. Then again, Kiva's alternate universe counterpart had an identical mech in the finale, so maybe there was a way to salvage it.

Coop is one of Da Boyz.
Let's see here...
 * Hammy? Check.
 * Big boned? Check.
 * Fights for fun? Check.
 * Operates and maintains a machine that by all rights shouldn't function? Check.
 * Has absolutely no concept of enuff Dakka? DOUBLE check.
 * Suspiciously similar Battle Cry? WAAAAAAAAAAAAAAAGH!!!

Coop is a Genius from Genius: The Transgression
And Jamie is his Thrall Search your heart, you know it to be true.

The whole show is Coop dealing with childhood psychological trauma.
Coop is actually suffering from Regression due to psychological trauma he doesn't want to confront, trapping him in the mental state of an eight-year-old (possibly connected to the absence of his father?). Note his obsession with 80s video games (which would have been all that existed around the time he was that age), pizza, fast cars, and robots. He also seems to have no concept or desire for sex, alcohol, or any social interaction beyond his one best friend. What is impossible to determine is whether Jamie is a figment of his imagination or really is his best friend and plays along with his mental state so as to not upset him. Either way, Jamie's constant presence acts as an enabler for Coop's continued regression. Worried with her son's illness, Coop's mom hired a therapist named Kelly Andrews. Having tried every conventional means of psychotherapy with other doctors, she hired Ms. Andrews to try something drastic. She enters Coop's world under the name "Kiva Andru", claiming to be from another time to help Coop become skilled enough to defeat the impending threat of the Glorft (the stresses of adulthood). She does this by playing into his scenarios via the use of action figures. Every episode is just an exercise they work through with all the toys Coop has in his basement, but Coop experiences them as wild adventures as we see them.
 * The people Coop meets on his adventures are wildly different and reminiscent of several franchises of the '80s that would have toy lines. (S-Force, the many robots in Magnanimous' arena, even T-Bot sounds like a plausible toy tie-in for Mr. T.).
 * The way Coop 'saves the day' in every episode is usually using childlike logic. (Using Rock Pops and soda in 'TV Dinner', randomly pulling out the Phoenix Force via button-mashing in 'Buggin' the System', saving the day with Philly Cheese Steak in 'Space Booty', etc.)
 * The lack of continuity in the way he destroys Jersey City every episode implies he only does it in his imagination, plus the constant defeat and return of the Glorft, because the stresses of adulthood never truly go away.
 * His childlike impulses are usually in direct opposition to her suggesting more 'training' (a.k.a. attempting to prepare for adulthood.) Even with her extensive psychotherapy, he is still resisting her therapy, pointing to the seriousness of the emotional trauma Coop is attempting to avoid.

The reason the Glorft/Human war started is because of Coop.
Stable Time Loop, anyone?
 * You're right. If it continued it was confirmed that Coop CREATED the Glorft. So he did start it.