In addition to it's animations, part of the cry against two-handers, I feel, is that they represent the ultimate melee weapon. For many people, it was where they started learning the intricacies of the game.
I've called it the 'piano' of cRPG weapons before, and I stick by that- two-handers are a building block for the other melee weapons. Because of that, most players are more familiar with it's animations and the little tricks you can use with them than others. That's a little advantage in and of itself that might not be considered when looking at two-handed weapons.
I'd like to add that I don't think polearm thrust results in the same stun that 2h stabs result in. Or at least, there's a different dynamic that triggers it. From what I can tell, both players moving toward each other during the thrust is what triggers the 2h thrust block stun. I don't think the same thing happens with polearms.
Slowing anything down at this point is ridiculous. Changing the animations would work, but hey, it might also hurt the balance.
Rather, changes to peripheral (kicks to buff one-hand versus them, animations on certain polearms to buff those, making other polearms heavier for use of weaponstun, etc.) things should be made- though I feel that two-handers will always have the biggest advantage against melee in one-on-one encounters.