Different body types: it's particularly jarring to see the human warrior and mage look pretty much the same... The Circle must've been a great fan of ourdoor activities, but even so!
Opportunity to gather a more diverse set of allies/recruits: overall, I like the approach to side with either the mages or the Templars. Fine. But are we really saying that there's not even the occasional weary group of apostates or runaway Templar recruits, etc. that we could find in all of Thedas?
More interaction: with minor characters - why not see agents rush about or have small conversations with them? (Scout Harding is an exception, but for the most, once you've recruited them, all you can really ask if they have an updates. Boooring.)
End-fight Redux: please someone take this up! After spending a LOT of effort into fortifying Skyhold, the impact it has on the endgame is nil. V. disappointing. Especially since Awakening handles a similar story quite well.
Mini-missions: opportunities to go out and do stuff as someone else, not the Inquisitor.
Playable missions for the Inquisitor, specific to their background. Like reconnecting with their Clan or being ambushed by an enemy of their family, etc.
The Evil Option: not just being a selfish a*** but trying actively working towards a similar goal as Cory. Don't mind if it sets the character up to fail as long as there's good role-playing potential.