Chris Moses mentioned speed and timing for instance. Like in some IT drills you ask some specific type of resistance or cooperation. But only in some kata do you specifically ask this type of cooperation (ok ok there's always some sort of cooperation but at least I try to get to a point where there's none). How many times do you perceive uke (and yourself too) switch gears during a kata sequence? I guess it's one pitfall of knowing in advance what's coming. At least I'm certainly guilty of some of that though I'm trying not to be.
I think you need more differentiation between different kinds of exercises: IT drills, technique drills, kata and sparring.
IT drills train the basic IT stuff. Technique drills train the techniques. (So for aikido: uke attacks, nage/tori performs aikido technique.) In both these drills uke is being totally cooperative.
Kata training requires uke to present you with a challenge, a problem (set of problems) to solve. Basically this is kata training of the koryu as described by Ellis Amdur in his books. I don't think it's feasible to put this kind of training back in aikido. Finding more ways to drill techniques makes more sense.
Sparring is the only training that has a truly uncooperative partner, because he's actively resisting you and trying to do his own thing on you.
Some recommended reading, especially the five kinds of drills (posted earlier in a different thread; think it was Don Magee): http://aliveness101.blogspot.com/200...-drilling.html