Wow. I have a LOT of suggestions.
1) I hate the whole 'complete the pokedex' quest. I think that once you see a pokemon, it should be registered in the pokedex. As in, I should get all info of the pokemon without having to catch it. Also, pokes seen in the Battle Frontier should be recorded too.
2) For catching a pokemon, I believe one should be able to catch them after fainting them. What do fainted pokes do? Dissapear into thin air? Geez.
3) Elite Four Champions should start acknowledging I am fighting them for the 2nd time! I hate feeling like a stranger when they already know me.
4) Random challenges from randomly generated Cool Trainers so that I get a chance to defend my title as the Pokemon Champion instead of losing it to Cynthia every time I defeat her.
5) Not having to deal with stupid $h** while trying to catch good pokes like Feebas and stuff.
6) Have a better storyline than an evil Team trying to take over the world.
7) All pokemon catchable instead of 'only one starter' or 'version exclusive'. Have only one version! Nobody wants to buy three friggen games.
8) Introduce a PC version. I hate the small screen of a stupid console.
9) All HMs should be friggen powerful or at least of some use in competitive battling. After all, they're HIDDEN MACHINES! People hide powerful stuff. Not annoying stuff to teach to HM slaves.
10) I agree with Jesus Christ above me.
And that is just the start of a veerrryyyy long list.