This is a really fun idea, but I don't think it could happen in the games, because Bonnie didn't get much development, if any, in the game (I guess neither did Caitlin, but I think its a pretty different scenario). Now if the games were to borrow Bonnie's development from the anime, something like this could make more sense.
Actually I think Bonnie displayed a lot of traits in the anime that would lead her to becoming an excellent trainer in the future. First, she was shown to be able to bond quickly with any kind of Pokemon, she didn't favor some Pokemon over the other, and she worked very hard to understand them and treated them excellently. Although she did like "cute" Pokemon, her definition of cute was very broad to include most any Pokemon and she wasn't superficial about liking Pokemon, she would bond with any Pokemon just because she wanted to be friends. She is also shown to be a hard worker who is willing to take risks (and sometimes be a bit reckless). She has relationships across the board that give her the ability to learn from a lot of excellent trainers, she enjoys watching battles of all kinds and has had experience watching trainers with all sorts of different styles. She is smart, but wouldn't over rely on tactics, because she has experience with and has seen how a strong bond can overcome a by the books strategy. She actually has been shown to pay attention in battles too, so I really think she would have gained a lot from all the battles she saw, and would continue to see at the gym. She even had some battle experience of her own that at times went reasonably well. Her maturity increased throughout the XY run and she went through a lot more than most people her age, so by the time she is ready to be a trainer, she has already mastered a lot of skills necessary skills and has a lot of experiences to fall back on. She is also very outgoing, which I think is a trait that would benefit a strong trainer and especially a champion. The biggest question would be if she really would strive to be that incredibly strong, because I think her biggest enjoyment is just making friends with her Pokemon, but of course as she ages she may develop a greater interest in battles. She definitely thought mega evolution was cool, so I could see her having a mega evolved Pokemon because of how deep her friendship would be.
I do think it would make perfect sense to see her in a region that isn't Kalos too, because she has already travelled throughout Kalos, so it would make sense for her to travel a different region. The biggest problem is that for this to work in the anime, the timeline would actually have to move forward, which it never has and for it to work in the games they would really have to rely on the anime development, which they very infrequently do. Anyway, I think champion is a very ambitious mark, I would guess something a little lower, but I do certainly think with her personality and strengths that she really could potentially be that great of a trainer.