I would like the following:
1- Fully customation your trainer. Clothes, hair, eyes, age, gender everything. I never really liked idea of starting as kid, which is why I liked Colosseu on GC - you start off as older teenager.
2- Keep exploration 2D-with-3D look, but have 3D battles. Probably will never happen, but hey.
3- Reduce HMs to at least five. Or, let us forget them easily without having to get HM Deleter to do their job.
4- Either Team Rocket, or Team that's interesting as Team Rocket. Ru/Sa has lamest 'evil teams', and D/P was worst.
5- Stealth Rock to be nerfed. It's silly that Butterfree, Charizard & Moltres etc getting whooping 50% dmg when switched in.
6- Get rid of grid system, and let us walk/run in all directions.
7- Bring back V.S. Seeker, or at least let all trainers to re-fight at anytime.
9- Wi-fi to have more features. Customation rules, 2 Trainers Vs 2 Trainers, Set Level (So if you want forceset Lv30, you can), simple item trading.
10- 'Mailbox' system, maybe? Will need use Wi-Fi feature but this allows swapping of mail over Wi-Fi, which would be nice.
11 - Make legendaries interesting again. I don't know about you, but I always liked stories of legendaries. It's just in Ru/Sa you get "robotic" animals, then in D/P it's "robotic" some kind of space/time/god, which I don't really like. I'd like Black/White to feature animal-based, less robotic legendaries again.
12 - Finally, even if it's covered in HG/SS, let us fight gym leaders again. It's silly how we could only fight them once or twice, then never be able to fight them again.
Well that's all... yeah I'm going to disappoint myself.