Although I think it does make sense to pull trainers from the games to throw in the anime (Other than the obvious Gym Leaders and stuff, I mean characters like May as she was the female protagonist Gen 3), it also isn't absolutely necessary either. It's really not the far from the realm of possibility that the anime could just create entirely new characters from scratch. If the reasons that we're holding off on being able to customize our character is just because the anime needs to have a single character to pull from, then I think priorities should be re-evaluated. Although it's not a feature that's necessary or anything, it shouldn't be contingent on what the anime wants to do, especially since it comes out after the games.
tl;dr Inclusion of customization shouldn't care about what the anime wants to do