Invincible/WMG

Allen The Alien knew Nolan was a Viltrumite from the beginning.
Allen The Alien has spent all his life working to oppose the Viltrumites, whom he hates passionately. He then comes upon Earth, where the people all look more like Viltrumites than does any other species we've seen. he then fights one of them, who displays Viltrumite-level abilities, and has a mustache. Clearly, he must have known right off the bat that "Omni-Man" was a Viltrumite, and might have even assumed that Earth was a massive Viltrumite colony. Since Omni-Man let him go alive, he kept coming back every few years, to try and determine the Viltrumite's mission. When he fought Mark, a possible non-Viltrumite with great physical powers, his superiors ordered him to inform the other hero of the situation, so the two could ambush and kill the Viltrumite together.
 * Actually, the then-chief of the planetary union Allen worked with was a repentant Viltrumite, protecting the galaxy to atone for the wrongdoings of his race. As this revelation comes right after the reader is shown Nolan's Heel Face Turn, Allen (or his superiors) may have thought that Nolan had already atoned, and Allen was supposed to keep tabs on that.

The Viltrumites could never truly conquer Earth anyway
Just the number of superpowered characters in the series proper itself is staggering, and then when you combine that with the fact that it's also part of the larger Image universe who have some massive heavy hitters living there as well the deck is already stacked against them. They've already driven off much larger invasion forces (from a species that even gave Omni-Man trouble) and now we have two Viltrumite hybrids on out side as well a Allen (who is quickly surpassing Viltrumite levels of strength). Furthermore the way that Omni-Man disposes of the original Guardians suggests that he knew that he couldn't win in a fair fight against all of them. Earth would finally be the death of the empire.
 * Jossed pretty brutally by the Invincible War, Conquest, and the Viltrumite War, though we'll probably never know if Omni-Man would've had trouble with the Guardians or not.
 * We know for a fact post Viltrumite War that they can't. The total count right now, is something like 46 living, loyal viltrumites. They flat out said that they couldn't conquer it, but they could (if they wanted), eradicate pretty much all life on earth in the time it took for them to deploy (look at Invincible War). Though this might be different with the Re-Invincibles (or Reanimarks, or Rean Invincibles, Reanimen made out of the dead Invincibles from Invicible war, for the uninitiated). Actually, they can't conquer much of anything anymore due to their numbers. It's vaguely implied that Humans are descendant of (or the ancestors of) the Viltrumites, hence the close genetic match and prevalence of super powers.
 * I wouldn't be so sure about that. True, the Invi-clones didn't manage to conquer Earth, but dozens of organized, adult Viltrumites would probably go through the heroes like hot knives through wet warm butter. And looking at Thragg, well... is there anyone who could fight against him and win?
 * Spawn, the Darkness, and that giant thing with claws all managed to take down an Invincible on their own, and Mark himself accounted for several, but those were mostly one-on-one or group fights with the villainous Invincibles - themselves crisis crossover level opponents on their own. And as we've seen from the rest of the comic, the Viltrumites don't exactly fight one on one when they don't have to. It would be a horrific methodical slaughter.

The Immortal is a Ti- Argh!
Sadly, the author of this theory appears to have vanished before finishing it. We may never know what it was meant to say.

The Immortal was Abraham Lincoln.
In his Origin, he talks about leading the people of the Americas, while a shot from behind shows a man in a stovepipe hat, speaking before a large crowd. Perhaps a younger, more patient Immortal was once the nation's most famous president - it would help to explain the unique deference Cecil shows him.
 * There's notes with it saying that his Origin was to make it canon since they had people theorizing he was and thought it would fit in okay.
 * Well, let's see. He looks the part. We have a scene where he's talking about a past life, where he was the president, and it shows the back of Abraham Lincoln's head. Also, he looks damn similar. Now, it's been said in the Handbook that we're not clear if he was Abraham Lincoln, or if he replaced Abraham after a while.
 * Also, upon Invincible's return to Earth, when Mark and Eve are The Immortal's guest, he tells a boring tale about his past about "Someone trying to shoot him in his head, and given death penalty for that" and "how sorry he was at having to fake his death and let the guy get capital punishment". He also makes clear who the guy was meant to be...

Darkwing is still alive.
Hey, we don't have the body. The Invinci-clone Darkwing pulled into the shadow reality was not as wise as core Invincible, and let go of him. Unfortunately, before Darkwing could come back out, one of the creatures there grabbed him - once he fights his way free, he will return, even more dangerous.
 * Seems likely, seeing as he took a crippled Invincible with him. Also, Rex Splode, the Mauler Twins, and Conquest are the only confirmed major character kills. Robert Kirkman Jossed it when he was talking about how sparingly he used character deaths (saying he only did it about 3 times, including Rex Splode). Also, we've seen characters come back from MUCH, MUCH, MUCH worse. The Viltrumites from when Mark reunites with Nolan, Angstrom Levy, Oliver, Allen the Alien, the Immortal (constantly), Dupli-Kate, the Mauler Twins did so once, Rex did it once, and we had BODIES on those.

The Great Thaedus is still working for the Viltrumites.
He founded the Coalition of Planets to gather all the resistance to their rule in one place. When the time is right, he intends to crush it in one fell swoop. He is the leak who told the Empire about Nolan's betrayal, and by taking orders only from him, Allen is playing right into his hands.
 * In Invincible 66, he is reluctant to show Nolan his true face.
 * ... And in Invincible 67, it is possible that troops in his employ were ordered to sabotage the effort to capture the Rognarr.
 * The problem is the fact that . If he's less noble than he seems, then the only realistic possibility is that he's aiming to take over the Viltrumite Empire, using the resistance as cannon fodder for his coup.
 * Well, he claims that he developed it. The only evidence he presented was a laboratory with people working on... something. Nolan has never shown a great deal of scientific knowledge, and even if he has it, took no time to inspect the lab.

Mister Liu cannot retain spirit form very long.
When trying to cross the ocean, he stayed airborne for too long, and fell, causing himself and his minions to drown. This is why they never showed up for revenge on Titan.
 * They have now...
 * Though, admittedly, Titan seems to be back with The Order for some reason...
 * The reason being that Liu doesn't run the order. Someone else does, and he considers Titan just as important.

Kursk is secretly behind everything.
We know that he's rather intelligent, but has trouble communicating with people who don't speak Russian. What we don't ket know is that he uses this intelligence, combined with near-limitless powers, to manipulate the entire population of the Earth, and beyond.

Mister Liu is Master Li.
The names are similar and Liu certainly has the power and underworld influence one would expect the Glorious Strategist to aquire, but the clincher is that his spirit form is a giant dragon. Clearly, he got this form by absorbing the godly powers of the Water Dragon centuries ago. His mortal body could not contain all that power, thus the need to project it externally.

The Order is a group of cyborgs who united to Destroy All Humans!.
The only members we see are Machine Head (self-explanatory), Mister Liu (robotic lower jaw), and Titian... who gained his position through violent treachery, and was rejected by the rest of the Order. With his stone form, the Order was not sure at first he was simply an inferior human - when they found out, they declared war on his operation (concern for the loose cannon Multi-Paul was just an excuse).
 * Uhhh, actually, we've got a ton of confirmed members with no robotic additions. I think the loss of limb comes with being a super-villain.

Rex Splode was created by the program that made Atom Eve.
His "secret origin" mentions that he was created by the government to be a weapon, and that's what the Atom Eve project was. Plus, his power can be interpreted as a form of matter transformation (just into energy, not other matter).
 * This makes their relationship a little sqickey, but at least they didn't know, and never had sex.
 * Never had sex? It was pretty explicitly stated they had plenty of sex. On the other hand, the Atom Eve and Atom Eve & Rex Splode minis confirm Eve and Rex weren't created by the same project. All the kids created by the "Eve Project" had innate powers, whereas Rex didn't have any powers before he was given some cybernetic enhancements. And in the Atom Eve mini it's revealed that all the other kids created by that project besides Eve were inhuman-looking mutants, which Rex clearly isn't. The only mysterious part of Rex's origin is the connection between his dad and the guy who gave him his powers.
 * They still may not be genetically related; the project could have used DNA from widely varied sources.

Controlling robots larger than a certain size is dangerous to Robot's mind.
This would explain why he never uses the bigger (seemingly more powerful) drone he used to defeat the Mauler Twins again.
 * Jossed. Robot has been shown controlling multiple robots of different sizes. It's just now that he has a body he prefers the bigger ones to ride in to keep his fleshy human self safe.

The wife that Omni-Man misses is Oliver's mother, not Debbie.
He only ever mentioned missing his wife after leaving her, and it was her planet, not Earth, that he stayed with to protect from the Viltrumites.
 * He admits to Mark himself that while he does love Debbie he sees her as little more than a pet.
 * This troper isn't very far in, but if by that you mean before or during his fight with Mark, isn't it somewhat implied he's bullshitting/trying to fool himself?

Anissa will try to seduce Mark.
After the end of the Viltrumite War, the stated goal of the Viltrumites on Earth is to breed with humans. However, Anissa, being a proud warrior race woman, is clearly shown not to be impressed by weak human guys. But Mark, the guy who defeated the second-toughest Viltrumite of them all, might certainly be an acceptable mate for her. So Anissa will try to get Mark sire a kid for her, which of course doesn't sit well with Eve... Some Unwanted Harem action will ensue. It's also likely that Anissa will later on undergo a Heel Face Turn, first of all because it's more likely to happen to an attractive female villain, and secondly because she is the only one of the villainous Viltrumites who hasn't been depicted as a murderous sociopath.