What I would like to see is a new perspective (Ezio is getting a bit old now - which is mentioned in the first half hour) and maybe multiple crossing perspectives. Perhaps Desmond could have a pair of ancestors in the same time frame, however one of them has defected to join the templars. And throughout the game the conflict escalates until the final showdown between two characters you have come to relate to. And no you wouldn't play this battle so you wouldn't know who would win and be kept in suspense.
Improved free run AI - a lot of missed jumps and no movement at all
Brotherhood could have more customisation (like shoulder pads, weapon type etc) and better control (they randomly spawn and run in, I'd rather if you were up high they would air assassinate etc)
Brotherhood ranking - I wanted this so bad where you could have like second in commands, mission co-coordinators, team leaders etc. This would have made me actually want to change assassin's colours (Black for leaders and me and white for the grunts - like AC1)
Of course to go with that each potential assassin would have their own stat set (subtlety, sabotage, organisation, intelligence, free-run, etc) which would make different assassins better at different roles and mission types.
Glances at what Abstergo is up to - many games have flashes where they show what the bad guys are up to and when but all that happens in AC now is we get told Abstergo seems to have certain plans. Of course I don't want them telling their plans outright, merely hinting and showing some courses of action - they were pretty much not present in Brotherhood at all (despite some emails sent by your co-workers)
The return of multiple city maps - Rome was good and all but it felt so empty since about 65% of it was countryside with small villages. I really liked the different styles of Florence, Venice and Forli and how they changed your freerunning style a bit.
Different weapons for different combat situations - I found myself just using the sword the whole game with the occasional switch to hidden blade for some targets. You have weapons strapped all over your body and many different kinds to buy, yet one can take down every opponent you come across.
Better thought out abilities for multiplayer - I play manhunt and now all my opponents are over level 20, they ALL have templar vision. Making effective hiding impossible when all four enemies have a sure find ability with only a 60sec cooldown.
And... I've ran out of steam for now