Theories

http://www.stwing.upenn.edu/~pdanner/resolute2.shtml

My prediction, I think they were going to make the new aliens supperior in technology and force. This would force humans and sapes to work together. While it would not be a harmonious alliance, they would have to learn to see past their differences in order to stand a chance against the new enemy.

Its a pity we never got to see more of the alien race, the only thing we really saw was that ship and the satelite - like device that they had on mars. It would have been awesome to see the show go on, but on the bright side, we atleast got to see the end of the Humans VS Neos saga.

It's been a while, but I think the missing planet was possibly going to end up wandering around the universe as a spin-off series (or at least a story arc). J.T. Marsh was going to be rescued somehow.

The main story was going to be the humans and Neosapiens joining forces to fight the new invading aliens, who were going to be very powerful and very alien (which is why their ships didn't even look like technology as we know it). The clone of Phaeton was going to be used to get the cooperation of the defeated Neosapiens -- thus making an interesting philosophical point about how a few differences along the way can turn the same basic character into a hero or a villain (the clone of course was the same genetically as the original).

To be quite honest, as far as a third season of Exo-Squad would be concerned, it is exo-squad, so the aliens would likely have to be fielding some type of techno-organic, or possibly living exo-frames. As far as pheaton, I doubt that Pheaton would be an ally, too much bad blood, besides, it seemed that Marsala was representing his people. Chaos might not be missing at all. It was a planet composed of dark matter, so it might just be cloaked. All in all, the show exposed the presence of other planets in our solar system, so these aliens might be from another world, but not necessarily another solar system.
As for Able, Marsh would get resued because chaos was populated and there were bound to be more ships helping move the pirates to Mars. I can see maggie and alec trying to settle down, and the problems between neosapien (Neomega) and human in a way not seen before. Kaz would likely have the same exprience as Colleen, and on his graduation day, another war could begin, and Wolf and Rita would likely still be with the fleet. With likely Simbacca in command of Exo-Fleet, there are bound to be Marcus style mistakes in the opening portion of the war, forcing Marsh to rebuild his squadron and along with algernon (and his GRAF technology) to resue those lost on Choas.
Nara is the ace in the hole, though, it is likely that Ketzer's storyline was meant to redefine human, as if to say that the third season would be a race war, but not between any of the sapient species.
It would likely have been more than one season of story, more like two.
But what do i know? I'm jut a fan.
(P.S. Cyclonus=Transformers/Typhonus=Exo-Squad)