The AvP comics are generally poor enough that recounting them isn't an experience too many want during a game experience.
One instance of the AI messing up doesn't undo the great Alien AI, especially when the game you're comparing it to was a step backwards in comparison to AvP'99.
AvP2's story wasn't so much better, it's just that the environments are much more co-dependent than AvP3's. AvP3 has a sort of linear progression that screams "VIDEO GAME", whereas AvP2 has a more believable setup that doesn't climax in one location in particular, but progresses more logically.
The thing that really sets AvP2 apart is the setup. A lot of stories (including AvP3) are just "HUR DUR RANDOMLY WE FOUND ALEENS". AvP2 actually thought about this and used the Pilot's telemetry from Acheron as a basis for finding LV-1201.