That's a bit unfair though, because Altair's animations were very limited by comparison.
Altair has 8000 motion capped animations... While drake has a lot of possible animations, how many "moves" do you think that Altair is lacking?
You'd change from the one runnig animation to the one climbing animation, whereas Nate will mix his running up with lots of animations, adjusting his feet slightly, and so messing up the launch-point for any climbing animations.
Altair has much more than just 1 running animation and 1 climbing animation, he has many many animations in between. He has lots of animations inbetween normal tasks that get run dependant on what you do, just like in drake. The difference being that Ubisoft motioncapped all "thinkable" moves that where needed, wheras drake tries to find a fitting animation in his library that can be combined with the current one.
The problem with nate is that he has to be at some predefined position for all his jumps to work, and since nate allmost never is right above that position he magically flies to some spot in order for the animations to kick off.
The organic result your talking about in the rest of your post, is more a case of you loving uncharted animation hype. There is nothing "organic" about mixing 50 animations when the actual movements are not based on physics, but upon scripting. Might aswell just run with motioncapture as that will give you a better result.
He is not moving more lifelike compared to Altair at all, while uncharted can mix around with several different animations at once, Altairs animations for everything thats happening are allready pretty motion capped perfect animations. I doubt that Uncharteds animations look better than Altairs more than on a few very rare occasions, whereas 99,9% of the time Altair will move seamlessly.
If uncharteds animations had physics in it, it would be much better, but right now the system is broken. there is no point in having animations being generated\mixed on the fly, when your not using phsyics but pre-scripted zones to make drake pull of his moves. The end result just insn't there. If it was physics based, hed try to jump the rock and maybe or maybe not he would make it, that would be more life-like and everything. But its not, he jumps, and he magically flies to the center and pulls himself up.
Try going up and down something a few times in uncharted, and you see how nate will magically fly to some "sweetspot" in the rock\whatever each time he climbs up, or down or whatever. Whats the point of being able to generate animations on the fly if there is only 1 way to climb everything?
Try jumping\climbing around in assasin, he never seems to be warped to the "sweetspot", the overall impression is that Altair seems to be moving very natural and true to life, whereas drake is being pushed around by the game to make things happening. Personally i think that uncharted system needs a lot more work for it to be better, because right now the pre-defined things in geometry and warping makes it look bad if you play assasins creed next to it.
Uncharteds system has a lot of things going for it, but it needs more work, and they need to get rid off all that warping and scripting.
But he's meant to trip over...that makes his animation look so great and realistic. He's an infallible hero. He's not a perfect spiderman who can climb towers at will.
He is not meant to be jittering and magically warping to the certain geometry points every time you try to climb something. Thats the point, Altair moves seamless and you have a very hard time spotting any form of warping between the jumps. Whereas nate is being warped to places every time he makes a jump or tries to climb something.