It was the little things that made AvP bittersweet. The actors left something to be desired, and there was very little backstory and building of the characters. They killed off two of the preds in like a 5 min period BY THE SAME ALIEN! They were both cool deaths respectivly, but c'mon. Gills death was alright, no real complaints there (except the tails length) but the pred (celtic) should have won his fight, or had a different fight prior to that one that it won. On that, the Celtic / Grid fight was pretty much the only Pred v. Alien fight, untill the big queen fight. The plasma canon was moot, Scar managed to kill 3 aliens with it (which was actually a pretty cool scene, IMO) but then lost it before it was ever used again.
I think that a Grid v. Scar melee fight (ala Celtic v. Grid) was very much desireable aswell, with Scar the victor, of course.
The infamous 'team-up' was... corny. It could have been done much better than it was, there was just something about the way Scar and Lex interacted that I hate, how the communicated and such, it would have been better to just have her sorta tag along and him more or less ignore her as he had bigger concerns and wasnt there for her.
I would have liked to see more pred hunting, which could have been done better during the surface Pred v. Drill team scene, which would have also built tension and given some much needed length to the film. Also this could have been just the filler needed so that there was a better amount of time for the alien cycle (from egg to adult) which happened in like 10 mins.
The aliens should have been built better, knocking out people one by one, also building tension and building up the alien. On that, the characters reaction to the aliens was poor. There wasn't enough surpise or confussion on what the hell it was, and not nearly enough fear portrayed by the characters towards them. Again, some filler for the movie could have been a moment where the people managed to get away and discuss what the hell just happened in some momentary safty, like traped in a room before another pyramid shift.
The Queen was done fairly well, IMO, but was just a bit to much like a Jurassic Park T-Rex, rather than an 'Aliens' Queen. Also the way they 'killed' her. They could have done something like Scar managing to land a killing blow with some weapon when the queen had impailed him and brought him up to her face.
The pred ship was too different and clean cut compared to what was seen in P2.
thats all I can think of that should have been different, at least for now.