I'll start off my controversial list, then...
Predator 2: The primary flaws were the over-the-top gangland plot and the government angle; they could've dropped them entirely and made this a bloody film noir.
Alien 3: More emotion, really. They could've really hit home on all of the fears and taboos we have in the final part of their trilogy. It was a missed opportunity.
Alien Resurrection: Make the Newborn a failed Ripley clone and play up the film's finale to fit the sarcastic Aliens angle it had taken up until then.
AVP: What SM said- get rid of the team-up. Some continuity would be nice, too; Aliens don't grow in minutes, and the Predator should be a destructive monster to behold.
AVP: Requiem: I'd have the film take place on the Predator ship from AVP, stick to Wang's intended designs, and have normal PredAliens to compliment the inseminating one. This had good sci-fi, horror, and action potential. It didn't deserve the Dawson's Creek treatment.