The way they "tried" to keep things together was lazy and halfassed.
Wilks having Drake, Vasquez, and Hudson in his squad. The Aliens still being on earth post Earth War and somehow the deletion of technology stops them from existing.......nevermind the fact that 200 years isn't enough time for people of earth to forget anything. People aren't going to stop telling stories or keeping records just because their computers went down. Never mind the fact that all these other corporations had caches of aliens off planet anyways. And a memory eating computer virus wouldn't affect old technology that didn't have computers in them. Took them back to the stoneage. Right.
The Weyland family owns the corps yet they need armies of personal security, mercenaries, and combat androids in Alien 3, AvP 2, AvP 2010, A: CM, to pull off their plans.
The problem was and has been (maybe not now but I have my doubts) been that for the EU Fox has never really cared about their EU concerning Aliens franchise. If they did they would have multiversed it along time ago or not come up with some of the stories they did.
Everybody looking for an Alien needed to only go to earth. Or LV1201. Or one of a dozen other overrun planets.
The EU has always been its own thing for me.