This is a bit different, as its really just my theories on the “flash sideways” in light of this most recent episode:
Maybe the flash-sideways is showing us WHY people are choosing the sides they way they are. Showing us that under different circumstances, people would me making similar choices to what they are doing on the Island.
For example, given different circumstances, Sayid would still be a killer for Nadia’s sake.
Ben, given different circumstances would sacrifice his power for Alex (weird when she’s just a student at his school [Side note: Rousseau never crashed on the Island, and is still perfectly sane living in LA. Does anyone else want to see how she would have ended up as much as I do?], and not his adopted daughter). Which is a major shift from his choices on the Island, but justifies why he would want to try to do the right thing currently.
Kate, given different circumstances, would still follow Claire around wanting to take care of her and her baby (that one is a stretch, but she’s following the evil people around).
Jack, given different circumstances, would still want to be the best leader he can be.
Locke, if he wasn’t dead, would have lost faith (does that even count?).
From that point of view, maybe it makes sense? But it doesn’t change that these still aren’t our characters. The characters we know were shaped by the Island at every turn, these haven’t been.
I’d also like to point out that Ben was still shot and saved by the others, and people were told that he wouldn’t be the same after that. AltBen went through that experience, while evidence shows that BenPrime very likely DIDN’T (judging by normal time travel / alternate universe theories).
Of course, I’m just going by the “normal” “time travelers create an alternate timeline” idea, which the writers deny. But we’ve got TWO timelines, one where the Losties are displaced in time and set off the bomb, which apparently doesn’t happen in the Prime timeline because the Island is still there. However, there is still evidence that the Losties were displaced in time in the Prime timeline (ZombieLocke giving Richard the compass to give to RealLocke, the picture shown to Sun with the Losties in DHARMA, people referring to the “Incident”, and so on). I’m just thinking out loud here, so the contradictions are intentional. It’s very likely that both Bens forgot getting shot and were “changed forever” and “lost their innocence”, and maybe that’s part of what the AltLine is showing us. Maybe that Ben can overcome his badness without having to learn from his mistakes that he can’t take back…