I want to see 2 multiplayer modes.
There are so many ways that could be awesome.
As for other, non-multiplayer things, more stats at the end of a mission, showing how many times any given power was used, how many people were choked out versus killed, showing who was affected in more detail than just hostiles and civilians.
A way to non-lethally take someone down after being caught other than sleep darts, maybe a bone charm for when you win the sword clashing thing, you can knock the enemy out with the hilt of your sword instead of knocking them off balance.
Enemies waking up after a while from being knocked/choked out in any way, and will be on alert with swords drawn.
More nonlethal powers, and a wider selection of powers in general to choose from, maybe about 3 more passive and 3 more spell-type ones, and instead of upgrading powers with a simple level up of the one power, leveling up aspects of powers, for example, clicking on blink would allow you to choose from:
Blink, increased range of blink (obvious).
Time slowed while holding the button and not pressing a movement key, like a weak version of Dauds, if this branch is upgraded fully (maybe level 3?), time stops.
You could have all branches fully upgraded, but of course, naturally it would detract from your ability to upgrade other powers.