Are we talking about a REAL reboot from the beginning (showing how he first got the omnitrix), or are we talking about a soft reboot, where we continue where we left off and just change a bunch of shit ( like they did with Alien Force and Omniverse).
If we're talking about a full on reboot, I'd have made characters like Tetrax and Xylene more promenent - ties to the alien origins of the Omnitrix are important, I think, and so is the fact that Max has ties to it as well.
I'd probably also bring up hints about Azmuth sooner, even if they never get to meet him until the very end of the series proper.
Give Gwen her own rogues gallery aside from just Charmcaster. I'm OK with keeping her magic abilities "alien" based, as the fact that Max boned a bunch of alien babes has always been canon, but the spells them selves should always just be spells. None of this Green Lantern construct bullshit like they pulled in UAF.
I'd also be good with introducing more plumber offspring that are around Ben's age, or at least other kids with powers ala Kevin and Cooper.
Keep Vilgax as a Juggernaut-like character. He shouldn't speak much, he should just wreck as much shit as he can in pursuit of the Omnitrix.
The same goes for Ghostfreak, if they choose to use him. He's probably the most powerful being in Ben's rogues gallery, and should be treated as such.