A lot of what I want has already been mentioned quite a few times. The VS Seeker for making rematches against other trainers easier, Secret Bases w/ WiFi connection, at least two rods preferably before you beat the Elite 4, Move Tutors, and I would really like to see the return of Pokémon Contests. I feel like with the new 3D graphics they've installed, Contests can be taken to the next level and hopefully this time with WiFi compatibility as well.
I would also very much appreciate, as Suicune mentioned, an integrated touchscreen layout a la HG/SS. The C-Gear was completely a waste a space and took up the entire touch screen in Black and White. Much less, I never even used it. So, a touchscreen that we can really put to good use would be a nice return again.
The "Follow Me" feature would be nice to have back, but it doesn't seem we'll be getting that here, not as far as I can see.