I see two options that I would be equally fine with (assuming the script is well written and well executed, of course.)
Retcon Version:
Retcons Alien 3 and Resurrection, and starts a new story taking place some time after Al()ENS. Involves Ripley and Hicks versing Weyland-Yutani.
Non-Retcon Version:
Takes place after Alien 3 (with Ripley dead), but way before Resurrection. Since there's like a 200 year gap there, i'm sure they could invent a new story in there with new characters. WY still trying to engineer aliens as bio-weapons, and new characters discovering the horror and trying to stop it. They wouldn't have to "retcon" resurrection, just ignore it since it wont happen for another 200 years or so.