...Uh...I really kind of doubt that Cyrus, Mars, Jupiter, or Saturn, or the grunts, are aliens. Cyrus just dislikes the world he lives in. He hates all the strife going on, and wants to create a world/universe free of strife. His goal sounds nice enough for being the top villain of the game, but, yeah, then there's the whole "I will become a deity!" thing. How he decides to go about his goals is kind of a downer, too (because then everyone, absolutely everyone, will die), but he does say that the world is too corrupt to make anything good out of it, which is why he wants to simply wipe out the world/universe and start over.
I don't know how you can go "beyond" messing with the time-space continuum, either. The villain Teams seem to outdo each other in every game (getting money, killing Marowak, and taking over radio stations, to attempting to take control of the very land and sea to make the planet either entirely earth or entirely water, to capturing creatures revered as deities, containing the suppose god of space/time and coming close to reformatting the universe). Blah, I think I rambled too much...
EDIT:
Team Galactic already appeared (well, Commander Saturn at least), at the very end of DP episode 36, "Secret Sphere of Influence!" and in DP episode 60, "The Unown of the Zui/Solaceon Ruins!".