Things I'm hoping for X/Y/Z, assuming "mixed" area w/ old and new pokemon:
1. New, competitive evolutions for really, really bad G1-5 pokemon.
2. New, competitive items for fairly bad G1-5 pokemon.
3. Evolite variations for attack/special attack, and maybe speed?
4. Multiplayer "Quests" that let you team up with friends to enter a "dungeon" and perhaps capture an over-leveled/unique pokemon. (Think a level 60 pokemon you can catch either with 6 badges on your own, or 3 players with 2 badges each)
5. "Legendary" or "non-legendary" random battle options.
6. Sleep Clause? on random battle options.
7. Release of more G5 Hidden abilities; maybe a new 2nd hidden ability? Alternatively, new evolutions and attacks for bad pokemon would work.
8. New Attacks, with a focus on fixing bad pokemon.
* "Call for Friends" - a tutor? move available only to "bad" pokemon that would let them summon copies of their 1st evolution? to turn single battles into double and/or triple battles (on your side), and let you keep your summoned pokemon if you have a pokeball?
9. "Uplearning" - if a pokemon learns a move at level x, it should have a chance of learning it post-battle at any level below x in which an opponent used it. For example, if the new fox can learn flamethrower naturally at level 60, and it's involved in a battle at level 5 where an opponent's pokemon uses flamethrower, and it survives (say, via protect), ad the opponent's pokemon is KOed, it should have, say, a 25% chance of learning that move early. This would allow us to have "level 101" move learning that could only be learned in this way. There should be an item that increases the chance to, say, 100% since this is going to be pretty hard.
10. Reoccuring NPC battles
* "local pokemon" battles, like fisherman that stay in the same place and "capture" random pokemon for each battle each day.
* "level growing" battles, where NPCs are randomly distributed each day, and each time you battle them their pokemon gain a level. Note: They should give you the option not to battle them, perhaps telling you the level of their 1st pokemon, each day so that you could level up small pokemon w/o fear of getting into an outclassed battle.
11. Your own custom gym. Choose a type, or pair of types, and have a special box where you can put only pokemon of those type or types. Have this info distributed by wifi/ir, and let you battle challengers each day w/ their in-game teams, and let you use your in-game team to battle, say, up to 5 gyms a day.
12. Customized in-game character. Obvious.
13. Continue BW2's "BPs" for random battles; increase the options for BPs.
14. Adoption Center - whenever you release a pokemon, instead it should go to your adoption center. Once a week, you should be able to go online and trade your last 3 released pokemon (filtered for hacks) for 3 random released pokemon from others. You should then be able to adopt one of them, re-creating the "choose your starter" moment.
15. Re-challenge the elite 4/gyms with a new team (6 pokemon lv 10 or under when you register them).
16. Rebattle gyms at any time, rebattle elite 4 at any time. New, random teams for each gym leader/elite 4 member. (IE, each time you beat them, they add 1 to their que, then randomly pick 6 pokemon from their maximum team of, say, 12 pokemon).
17. Ribbons return. I'm just saying, it's nice to get ribbons to help distinguish your pokemon.
18. In-game, legit cloning. Probably costs lots of BP, but the ability to clone your best (non-event) pokemon in-game would be pretty awesome - even if it only comes out as an egg you have to re-EV.