I agree with the comments above on a dynamic disposition system. This could incorporate elements of 'alignment' (depending on the main factions in the game). It would be nice if there were more than just two main factions like in Skyrim - some Game of Thrones style intrigue with different houses would be nice, especially if there is a general civil war brewing (which seems like where the empire is heading).
This disposition system would not just be good for side quests, but also to gain allies, followers and yes, even romance.
What would be really nice is to take the roleplaying to the next step, allowing a player to build up their character's position in the game - allowing them to buy (or be granted) ownership of a piece of land on which they can build/upgrade their own holdfast/fortified manor. They can recruit followers (through side quests especially) and have these NPCs populate their holdfast. The more customisable this is, the more energy people would put into the game (I can imagine all the mods for special furniture, wall textures, etc). Pack rats (like most of us) could actually enjoy the collecting of bits of art, tapestries, random books, etc to decorate the place. If this comes out after the Oculus Rift is available, that could be quite something, having your own manor house/fortified tower/country estate to walk through, interact with your NPC followers/friends/lover/family.
One more thing that would greatly improve the series - try to give the NPCs some real personality. The NPCs in Skyrim really seemed like carbon copies of each other. The Witcher and Mass Effect series really brought the NPCs to life and this would be nice to see in Skyrim. I'd like to actually care about what happens to the old warrior in the tavern, or the merchant woman in the marketplace, and for this they need real personality.