The AVP 1 Aliens had their flaws, too. People just look back on the game with fond memories, that's all. Not sure if the sub-forums here can be trawled back for criticisms of it, but there were more than a few at the time.
Nothing major. Not as far as the AI versions are concerned anyway. They occasionally get stuck on things.
I'm not looking back, ether. I just went and played through the first three levels of the Marine campaign, followed by some skirmish. My memory is five minutes old.
There were some things that were off. No hatching eggs. No chest bursters. They were a bit too noise. Screeching every five seconds and such... But honestly, not much else. They did what they were supposed to. Get you on your toes.
They were nicely fast, but an argument could be made that they were almost too fast - and when you play as them, they feel like they're sliding on butter, but few, if any, games get the first-person 'running bounce' thing right, much less creature-playing ones.
AvP2 improved some of the elements of the Alien player's control. I'd ditch the incredibly silly superman-alien pounce, but the speed was more evened (maybe a smidge faster.)
I feel like an idiot right now though. I went in there to record some commentary and put together a video talking about specifically what Colonial Marines should have taken away from the legacy of Aliens games out there already, using examples from AVP 99 specifically... and then after I got out of the game to check the footage, I didn't have my mic detected by Fraps, so it only got the game sound. DOH!