Hilda not appearing at all (not even in Pokemon Generations! What the hell!) Has unnerved me since day one of Best Wishes. I honestly wonder if it's because she looks similar to Dawn? Probably not, but that's what I've thought since the beginning...
Before Cheren appeared in the anime, I had desperately wanted him to appear. Like way before Black2, and it was a shame he didn't appear until the very end of the BW non filler saga.
What else...
The Hoenn Elite Four, and just all the Elite Four not showcased in general, really. The only sagas I recall had the entire Elite Four shown was Kanto and Sinnoh... what a pain.