Personally, I think the Anthology assembly cut is probably more or less the best version of the footage possible. I prefer the oxburster to dog, as frankly having it come out of a pet is a step of nastiness too far for me. And Alien 3's other various flaws - that mysterious egg, bumping off beloved Aliens characters in the intro, some hammy performances, storyline wooliness, probably more I'm forgetting - are fundamental production problems which couldn't be fixed in the editing room.
The first two films, on the other hand... I've always felt the buildup to discovering the derelict in Alien dragged on for too long, and it seems there's some more killing footage out there (Brett's being the obvious one; I think they recycled some of Parker's for the final version). Some other changes I'd make, like a longer cutaway between Ash's prosthetic severed head and Ian Holm's talking equivalent, and a bit less strobe and more of the alien when Ripley's making her way to the Narcissus. And more basically, I've always had the feeling that there's more cool stuff lurking in the reels.
And Aliens, I'd have more footage of... the aliens. Shocker. On the umpteenth viewing it seems like the marines are being attacked by smoke machines more than anything else. One big improvement I'd love is seeing more shots of humans in the same frame as their assailants (which is also a major problem with The Terminator), but I'd imagine there wouldn't have been much of that left on the cutting room floor.
