I still do not understand the reason why the episode Goodbye and Good Riddance is non canon and exists in an alternate timeline even though the episode was pretty much in line with the main timeline (through the fact that it shares many similarities toDestroy All Aliens) and there is not any thing that is non-cannon about this episode. Ben returns back into Belwood, fights threats from earth or space (as presented in the flashbacks of Omniverse ) and removes the Omnitrix and does not wear it until four years later. Then, the events of Alien Force and Ultimate Alien occur.
This isn't canon because it's a "What if?" episode, which don't take place in the canon. Ben's parents learned of his identity in AF, and here they also learn it (and he has a dog). Gwen also transfers to Ben's school, which doesn't happen in the canon iirc.
Edit: This post strongly reminds me of this comment: "Yeah me too I think it's cannon but why is it in another dimension (timeline)? I don't get it. This should be cannon, there's nothing non-cannon about it. Ben returns home, fights stuff (as shown in Omniverse) and let's go of the Omnitrix. Then Alien Force/Ultimate Alien happens. Why non-cannonise this episode? It's as cannon and as in the same dimension (or timeline) as every other episode!".
Oh yeah, you are right, I forgot that. He was restored to life. But think about it. So far till Malgax Attacks, Vilgax was alive. And the Ben 10,000 timeline is the same as the main timeline at least till the end of Omniverse. So, obviously, if the timeline is the current future then that timeline's history so far matches with the main timeline's history.
So Ben's history up till end of Omniverse is same for both timelines. This means that if Vilgax died in Goodbye and Good Riddance, Ben 10,000 timeline would have separated off then itself and never become the current future.