Too late for Co-op, if that is just "patched in", it'll be a total mess.
They can add a much wider variety of spells. Hell, any veteran mage can tell you that constant damage spells are often better than instant damage spells. Back in morrowind, it was far more efficient to use
5 damage for 5 seconds over
25 damage for 1 second. Maybe that's why some of those higher tier spells are so stupidly expensive? Scaling would be nice, too.
Not so much adding as removing, but lockpicking... Really? Combine it with Pickpocketing and call it security. Also, add something new... like tumbling. Call it acrobatics for old times sake. It's not trained by just jumping, though, but by doing some kinds of maneuvers in combat. So... add some kind of dodge roll capability or something, more than that silly sneak run thing.
Smithing could use some love. And by love, I mean proper implementation. This has been done to death, look it up.
Where my spears at?
UI needs too look nice. And let me sort it, darnit! PLENTY of unused buttons when at the UI screen!
Possible to add viewable character in the equip screen? Kinda like morrowind did? Not necessary, but a nice fun touch.
Perk trees for races would be nice. Say, every 5 levels, you get a racial perk? Branch it in a way so that you can't max it out, even at level 81. Obviously, perks would be gained retroactively for pre-existing characters.
You know that follower AI overhaul mod? Adopt it. Make it official.
Hell, while you're at it, get those guys who did the comprehensive bug fix mod and HIRE THEM. And then have them fix all the bugs.