Wait, so Team Rocket fear them despite Team Shadow being in another galaxy? I mean, call me slow, but that honestly is problematic in a way. Like, if Team Rocket knows of them, then others should as well (secret police etc.). Now, again I'm not saying you can't make this work, but if Team Shadow is a bunch of humans that control another galaxy and Team Rocket is somehow aware of their existence and is scared (implying they know what they are capable of) then I have to say that it's going to take a bit of explaining to make it all work.
Ash being in his teens at the beginning of the arc is fine, but keep in mind any development from his 10 year old boy self that is relevant to how he acts now needs to be touched upon, as well as morphing him as this goes along.
Also I'll put this under spoilers for the leader,
Overall, be careful not to go out of bounds in the universe without explaining why you can in the first place. Otherwise, I'll the flag of "Continuity and impractical" will be thrown. Also, is this going to be a long running fic, just curious?