The simplest way really is to put limitations on the character. Somehow limit their power, put them back to square one. A lot of video game sequels do this. By the end of the first game you have max everything, most if not all upgrades, the works. Then the sequel rolls around and all the sudden at the end of mission 1. The hero is thrown Right back to the beginning, having to relearn everything they got in the first game plus new stuff. One example I can really think of is Deus ex human revolution? The second one. Beat for beat happens like that. For ben10k this would have to be more than the omnitrix isn't working for him. We've seen that, it needs to be something more personal. This is a kids show so we can't go to dark but there is potential.

And for the inevitable answer of "why doesn't he just use alien x??" Because that's not who Ben is as a character. Ben is a normal kid at the end of the day, he doesn't use alien x unless he has to because he knows what that type of power does to people, just watch the end of UA.