Alright guys, we can keep alien³ and everything will be alright. All we have to do is explain away the bullshit that happened; that shortly after they enter into hyper-sleep a team of predators interested in this kick ass family decide to kidnap them. Ergo while they are asleep they are taken and replacements are put in. aka cheap clone knockoffs, however to make things interesting(and because predators are dicks) the predator decides to leave a few eggs on board. Bang, boom, thank you very much! We now have an explanation of why the eggs were there, why the facehugger makes no sense, why bishop pusses out, and most importantly of all, how the dumbasses from A|R were able to get blood samples of Ripley's DNA. They stole that form the predators sometime after finding their crashed ship. cough, cough, AVP3.
How's that for some serious continuity bullshit.