Amanda was rescued and lived her life. Future Comics and videogames aside, that's enough. She found out what happened to her mother, and likely realized that she lacked the resources and connections to find her little needle in a stack of space. She moved on, and did what Burke said she did. Now, it's just my opinion, but I personally don't see the need to go any further in-depth with her character. It's certainly not film worthy.
As for Alien 3. To some it's great. To some it's terrible. Either way, after the different cuts, it's as good as it's going to get. It was made, it has it's place. Retconning it with something else is just like probing around in an old wound. For good or bad, it's in slot number 3. Best not to pollute it further with even more craziness like retconning.
With regards to the future of the franchise on film, somebody in charge needs to remember that it takes place in the future. Humans are working in space. Hypersleep is a reality. The money and manpower apparently exist to send regular people across vast distances, just for Ore. Something tells me it's quite possible for people other than the Ripley's to run into something nasty out there in the dark. I'd like to see some new characters, in new situations, that don't involve the past, or over-emphasis on artificial intelligence. We've yet to see the future, post Ripley. At least, not one that can be taken seriously.
