Personally, having just switched to a two-hander on my stf character, I feel the current two hand thrust animation is perfectly in line with the balance of the other animations.
The fact is that the original 2h stab animation was unchanged from later versions of the original, singleplayer only Mount & Blade game.(1.011)
I played from just before the release of the last version of Mount & Blade, through the beta of Warband and obviously up to now. During the beta I had a chance to observe the rapid and repeated revisions of the old, robotic, years old animations made before the expansion. All the animations gradually improved and became more human, and more believable.
Except for the two-handed stab animation.
This one didn't change at all. I guess the devs had better things to do, but the way in which this animation conducted itself was fundamentally different from the thrusts of polearms or one-handers.
It begins primed from a high and straight angle, the tip far in front of the swordsman, and is held there in a pretty unnatural looking position.(robotic, as I've said)
The animation stabs out to bring the blade out as far as the arm can possibly extend, almost as if the person didn't intend to bring the blade back at all. Compared to all other melee animations, it offered a massively better range per point of weapon reach. Warspears are questioned in their ability to outrange a greatsword thrust.
The nature of two handed weapons does improve the reach per length of the weapon compared to polearms. Instead of holding just before midlength as in a polearm, it is delivered with a grip at the end of the weapon. Onehanders are even better in this way, but they are less controllable at an earlier point of range/mass.
A game that uses realism/physics and accurate to the eye hit detection, should not feature any animation that does not conform to the realities of the human body.
The old twohanded stab was ridiculous for reasons stated. It was a dinosaur surrounded by updated animations. The new animation looks excellent, functions effectively, and feels fair.