Migration
I don't know why people are so worried about migration. If Nintendo wants migration, they will invent a way of doing so no matter how much stats get overhauled. I mean, just look at how you can find every type of conversion software you need for anything. You really think that's not going to be possible with Pokémon? Give me a break. And if they won't do a migration, just play the new game anyway. It's sickening to me how people got so upset at 3rd gen games for not having migration that they didn't realize any of the cool new stuff they got to work with until the next generation. You would still be able to play 4th and 5th gen WiFi matches if you prefer the old rules.
Stats
The stats system right now is extremely messy and complicated, not to mention broken in favor of certain Pokémon in certain metagames over all others. Whatever happened to the first two generations (when I got my link cable and actively battled everyone I can find)? The way I see it, everything's just so complicated and power creep, ability creep, feature creep, and every other creep gets in the way of enjoying your Pokémon. It's just not fun anymore unless you're doing something like random battles with random teams, or Balanced Hackmons, or something to that effect. I just want to grab my game and have fun, not spend the next 3 years breeding for movesets, IV's and Natures to battle online against everyone else who spends all their time doing the exact same thing. What's the point?
Competitive Battling
To the people who will be upset that competitive battling won't be possible the same way again, let me ask you this. Would you rather just spam a certain entry hazard that makes a large number of very good Pokémon unusable? Or do you want to use Choiced attacks to OHKO your enemy before they OHKO you? Or how about wall for ages with Blissey? I could go on and on but you get the idea. And if you prefer the old system, why not play Black/White 2 on WiFi battles? I mean, people still play 4th gen WiFi matches, and everyone will continue have their precious Smogon and whatever else remains. I don't know about you, but I would welcome something different than the usual GlisBliss, DrizzleToad, Balloon Heatran, Toxic Orb Breloom, and the like.
Evolution
I liked how there were new tools in 2nd and 3rd gen that expanded on ways you can raise your Pokémon. But right now, it's way overdone. You have to find way too many obscure, mostly useless items and hold them on the right Pokémon and trade them away to complete someone else's Pokédex. This also makes a lot of gameplay entirely pointless and tedious. Why can't we just have simpler evolutions for all Pokémon? I also wouldn't mind certain "corrections" to older Pokémon in this way. For example, female Kirlia into Gardevoir and male into Gallade. Miltank's eggs should be able to hatch into either Tauros or Miltak. Male Cacnea into Cacturne and female into Maractus. Luvdisc evolves into what is CLEARLY a Luvdisc evolution. You get the idea. And get rid of baby forms and let them just be the first stage. What kind of moronic idea was that, anyway?
Types
The elemental types are broken. Some have way too many weaknesses and others just make most other types completely useless against them (*COUGH*DRAGON*COUGH*STEEL*COUGH*). In second generation Gamefreak released Dark and Steel types, and they were only there to make Psychic and Dragon types not too powerful. Of course, back then there weren't too many attacks to attack Psychics (Signal Beam) and Dragons (Icicle Crash) that could have been made, but whatever. Developers never really rebalanced the types, and never added any new ones either. That needs to change. Sound, Data (Porygon) and Light could be new types, and I'm sure a lot of people have other good ideas.
National Dex
How about an evolution family based National Dex? And no, I don't mean the Johto Dex. I mean something that actually fixes 440 Happiny evolving into 113 Chansey into 242 Blissey.
Abilities
This was a good idea in R/S but most Pokémon had really ****** abilities. In 4th gen some of these Pokémon got slightly better secondary abilities. In 5th gen many Pokémon got significantly better abilities, but still, for the most part, the vast majority of abilities are useless.
Moves
Some moves are in every competitive set while the vast majority of moves don't get any attention. I'd like to see more varied moves (like different type entry hazards and more hazard-clearing moves).
Natures
I guess they can make breeding for natures easier.
Shinies
See above. 1/8192 is too low a chance and they can make getting these Pokémon easier also. Not too easy, but even a 1/256 chance would be reasonable. The way they organize the game data, they have separate normal and shiny sprite data and separate palettes for every single sprite. They could easily be more efficient reducing this to one sprite and a flag for normal/shiny that would pick the respective palette.
Gender Differences
This was a great idea when D/P came out. So why not do this with more Pokémon? Everything has a male and a female sprite and normal and shiny stored separately along with palettes. Why not make good use of that?
Items
Prices, availability, restorative ability, etc. can be reformed. You spend ¥700 on Super Potion to heal 50 HP, and ¥200 for the same thing? Multiple items that only heal one thing? Evolution stones can't be found?
Mail
Completely useless gimmick since Generation II. Get rid of 'em!
Levitate
It could be a separate attribute so Pokémon can be dual typed and still be immune to some attacks like Earthquake. And even airborne Pokémon shouldn't be immune from some Ground attacks like Mud Bomb.
Ghost
Ghost being immune to Normal might have made sense in 1st Gen, but now it doesn't as much. It's also immune to Fighting, but I don't see why Aura Sphere and Hyper Beam can't hit a Gengar for damage, especially when ghosts should be susceptible to energy bursts. Meanwhile, Metal Claw does hurt Gengar. Something needs to remedy this.