What I want to see:
Put the VS Seeker back in the games.
Most customizable use of the touch screen. DPP have done this best so far, then HGSS took it a step back by forcing the menu on it. And now BW have stuck that C Gear or whatever on it. I would like to be more like DPP where I could put things on the bottom screen like my party and their health, the region map, number of steps you have taken (great for breeding), and so on. Make it customizable again so I can put what I would find most useful to the situation down there.
Add an option to remove that low health beep already. It's been annoying since Gen 1, and only now in Gen 5 have they done something with it. Sadly, what they did was make it worse by not only masking the current battle music with a constant "BEEP BEEP BEEP", but now it changes the music completely. Boo! Just a simple option added to the game, low health beep with the settings beep only/beep + music/none would be a fantastic.
Do something with the damn HMs. I still like a solution I thought up a while ago best over other ones I've heard (which are usually using items). Just let any Pokémon in your party use any HM move they can learn outside of battle without taking up a move slot. Since it's not using a move slot, you can't use it IN battle, but you can still use it OUT of battle. So you can still use crap moves like Flash, Defog, Rock Climb, and Cut outside of battle, but you don't have to gimp your Pokémon's in battle move list with them (or carry around an HM Whore at all times). And the moves can still be put on TMs (TMs are now infinite use, so they are basically the same thing as far as teaching Pokémon a move goes) so if you want some of the good ones (such as Surf and Waterfall), you can still add them as a battle move.
Alternatively, let us DELETE HM moves! In Gen 1 it made sense to have them be undeletable, because you could carry only 20 items total, and that included HMs. So you would use the HM, then deposit it into your PC so you had more room in your bag. And if you had been able to delete a move, you could potentially get yourself stuck. Say you Surf to Seafoam Islands, and then delete Surf off your Pokémon for Hydro Pump or something. Now you can't Surf to leave. You also don't have a Pokémon that knows Fly, and you don't have the Surf HM or Fly HM in your inventory. Congrats, you're fucked!
But ever since Gen 2 when you had a special TM/HM section of your bag so that you always had all your TMs and HMs with you without running out of space, there was no need to make HMs be permanent without the Move Deleter because you could just take out the HM again if you needed it. Because if you were in the above situation, you would just go to your HMs pocket where your Surf HM would always be and just reteach Surf to a Pokémon. So there is no longer any need to make HM moves require a Move Deleter to be deleted.
They should put the auto-level feature back in Wi-Fi battles. It made it so much easier to just play a battle on fair ground (100 VS 100 or 50 VS 50; no 30 VS 70 unless you wanted it that way). They also stiffed over the breeders who now can't see their Pokémons IVs without using a pile of rare candies. It's like they wanted people to use PokéSAV instead of raising their Pokémon in the game.
And last but not least... No MMO. There is no benefit to be gained in this franchise by making a Pokémon MMO. We can already battle and trade online which is what these games are all about. They have all the online functionality they need, so don't shit all over the franchise by putting other players in my single player overworld exploring and Pokémon catching.
Mana Fiend said:
The ability to both withdraw and deposit pokemon into boxes on one menu, instead of having to move in and out of seperate menus.
That's been in the games since Generation 3. Instead of "withdraw" and "deposit", select "move". Now you can move Pokémon between other boxes AND your party all in one screen. There's also a button in there you can press that turns your hand gold, and then instead of selecting a Pokémon and asking if you want to pick it up, view its stats, change its tag, etc, you can just press that button (in Gen 3 GBA games it was Select, and in Gen 4 DS games I think it's X, maybe Y) and then it automatically picks any Pokémon you select (or puts them down) without asking what you want to do.
It's really quite awesome, except in Heart Gold and Soul Silver which made the option extremely unintuitive somehow. But hey, that's what Gold and Silver do: shit on the franchise. So I'm not surprised it managed to ruin a feature that has been working perfectly since it was added.