I'd like to see a few types changed, such as Glaelie to Ice/Dark and Celebi to Bug/Psychic (yes, a Bug-type legendary). I had a list a few thousand posts ago...
Also, with the type changes, I'd also would like for more diversity in the the already-existing legendaries. I liked how the last two generations made them masters of something in the universe, and I'd like for some new combinations to be made. For example, Mew and Mewtwo can represent natural vs. artificial. Mew can have form changes that will change her learned attacks upon environment (such as aqua form in water). Mewtwo, being manmade, can have his defense, special defense, and special attack raised in sacrifice of speed and attack while wearing the armor as seen in the anime.
I've thought it over, and we don't have to demote Heatran down from legendary status. He/she could be the master of the core, which would mean that we should have two more legendaries representing the crust and mantle.
Variations instead of shinies, please. Shinies have became overrated, but variations will encourage even more collecting.
I expect a lot of changes in this game- everything from type changes, better gender ratios, more abilities (I'd like to see all Pokemon have to positive abilities and one negative ability), new types, different methods of obtainment (no more breeding with incenses, but to evolve Slowpoke you will need a Shellder [perhaps maybe just a form change for Slowpoke?] and to evolve Magnemite you will need two more Magnemite), some species merged (mainly referring to Nidoran being one species), and new evolutionary stages (such as finally a Kangas, a male evolution of Kangaskhan, a pre-evolution of Tauros and Miltank, a Doduno, a Dugduo, and so on and so forth...)
