Hmm, well here goes some of the things that have been on my wishlist. This topics too big normally for my computer -_-
Houndoom evolution, Houndread. It just has to be done, he needs to be a Cerberus. Maybe a biting attack that hits multiple times. Plus, fire need an overpower monster to bring em back haha.
A change to how the pokemon league is done. I would find it much more interesting if you actually had a tournament based league, so you can't prepare for it, and so it changes each time you go through it.
More even with special/physical moves for each type, so for example physical water or ice types can still be good.
Maybe a legendary with 3 different types. It sounds odd at first, but it would definitely make him pretty interesting. Imagine a Fire/Water/Grass type.
More challenging foes. No more Fisherman Frank with 6 magikarp, or Pokefan Paul with 6 Pikachu. I'd like to see alot more trainers with 6 pokemon on them, because heck, it would just make alot more sense haha
Im guessing that the next pseudo legendary will be Ghost/Ground. Because they have had a pattern, dragon, then a physical typed special guy (Dark, Psychic).
If they do have a team, have them succeed in their evil plan. Then have to battle to turn things right again. (imagine if dialga/palkia werent stopped?)
Trainers that actually walk around, change areas within a route, etc.
I think thats about it. I do want more evolutions, but i feel that is the one i want more than any haha