Hm, what would I have done differently...?
General:
A storage chest added to Skyhold (Haven and Skyhold preferably, but in case of Haven I can live without it).
Helmet toggle being enabled for each character individually. Some characters look actually good/better with helmets/hats.
Crafting:
Craftable Skyhold outfits
Salvaging of items for resources as well reverse-engineering items for schematics
Dyes to allow you to avoid the less desirable colorschemes
World/exploration:
A far more interactive world. At present it feels really static, you can notice that especially in the Hinterlands when you free Crossroads and the villagers don't respond to the mages & templars fighting there. Being able to sit in chairs in taverns or on your throne would also have been nice.
Exposure to dangerous stuff like red lyrium should have an effect on your character & party members unless you take precautions (-> war table operation?)
Somewhat fewer side quests in favor of more elaborate ones. The current fetch quests are ok as fillers, but there are too many of them and some don't really seem to fit. Again, this is most noticable in the Hinterlands.
Giving Skyhold upgrades an actual purpose (I assume that was meant to be the case but got cut for whatever reason).
Combat:
Fewer VFX in combat, especially for non-mages. Sometimes it's too hard to see what's going on and do we seriously need our rogues to glow purple?
Weapon swapping in combat
Companion tactics with greater complexity like in previous games
Auto attack option outside the tactical camera
Skills:
Fewer restrictions by keeping weapon skills mostly separate from classes & more combat style choices (single one-handed weapon, dual wield option for warriors).
Return of actual non-combat skills that require skill points rather than Inquisition perks, etc. Let me choose whether I want my character to be a beast in combat or trade some combat ability for additional options in other areas.