If she came back as a main character I strongly hope that it's alongside Kate rather than pushing Kate back off the show. Having the two of them together would be an interesting dynamic.
As for what's happened to her, I figure she could have managed to get randomly teleported to a very remote location, and would be in a serious mess that would take a long time to heal from, due to the bad teleport. It seems that serious injuries and the need to heal break down her mental conditioning, so she needs to keep hurting herself to stay as herself. This continual warring of her own personality and the superabnormal mental conditioning would make her stay away from civilization as much as possible, which is why she's afraid to return or make herself known. (Obviously she gets found or is driven to go home eventually, for some reason.)
I suggest that Ashley's abnormalities would need to be negated (to stop her from going crazy) but the process won't be 100% effective leaving her with some handy remnant.
Also, I'd like it to be drawn out as a B plot over a few episodes so we don't know for a while whether she'll survive and be returned to humanity (or close enough) or whether she'll need to be locked away or put down for her own safety and the safety of others.
It would make for some great scenes, with part of her being Ashley Magnus who needs her mother, and part of her being a supersolider still having unfulfilled orders to destroy...
Also it would be best if they didn't preface the episode where she's first found with a bunch of recap stuff that makes it obvious that Ashley's about to return. If they must, they can do flashbacks *after* she's found. (for all the people who started watching in season 3

)
How did this post get so long??
Oh, the shapeshifter idea is kinda nifty, but nothing would beat having Ash back to her usual tricks (alongside Kate), after a significant amount of difficulty being restored.