I'd like to see Gestalt made core, with classes specifically designed to be combined with others-- so that there are both fewer exploitable combinations and fewer sub-optimal choices.
With that, I'd probably like to see fewer classes, with the varieties of base classes in the game now represented by specific combinations, and maybe combination specific feats that shape a character.
I would like to see armor reduce damage, instead of making it more difficult to hit. I know it's a sacred cow of D&D, but the armor system in Alternity was one of my favorite features. I want a Class Defense Bonus.
The big, futile hope is to see the death of all subraces, with cultural differences represented mechanically, if at all, by changing things like Favored Class/Gestalt and different weapon proficiencies.
I'd like a more robust template system for PCs as well as monsters, perhaps as part of the above futile wish. I'd like to see a wide variety of relatively minor, LA +0 templates, as well as planetouched templates, ancestral templates, and even character background templates.
More races, particularly more races that are more distinct from the Humans. I want Orcs as a core race, and Half-Orcs treated like a hybrid race, more like the Half-Elf. I don't want to hear "they're supposed to be a simple race..." ever again.
I'd like to see a bigger divide between Arcane and Divine, both mechanically and in flavor.
Less dependency on magic items. Not magic, just magic gear. I'd like to see PCs develop more extraordinary and supernatural powers on their own. I'd like to see spellcasters have some less flashy, less powerful all-day powers to complement their raining fire of doom. I'd like to see non-magical characters capable of holding their own at higher levels, and developing beyond human (or metahuman) limits as they gain power.