From a technical standpoint, AvP2 was better. Better graphics, weapons were more streamlined, more character interaction, an actual story.
But I still think that the 1999 game beats it. With aliens popping up almost everywhere and humans shooting everywhere in panic when an enemy appeared, it really had this fun, chaotic nature to it. Also, one thing which made that game more awesome than its sequel were the bonus levels. I loved being able to retrace the the levels of other species, sometimes going in opposite directions or taking other paths. I know that the story of AvP2 did not allow for this to specifically happen, but it's a terrible shame that they had no bonues stages whatsoever. The Xenoborgs were a fun addition, and the combat always seemed more frenetic than in the sequal.
AvP for PS3 just didn't have the spark of the other games. Repeatedly having humans facehugged or ripping out aliens' tongues got old after a while. The storylines were way too short, and everything seemed so flat. I've honestly only gone through the single player mode once, and I'm not too motivated to do it again.