I actually agree that this is the most logical twist they could have used. For the same reason you say, too confusing. I mean it already kind of was. And yeah, it's be interesting, but the emotional connection with each character becomes harder for the audience.

I'm wondering what triggered Olivia's memory. 'Cause if the amber verse/s are the red and blue overwritten and Peter has been back for a while now, why are the memories taking the time they are to trigger? Or you could be right, maybe it's been a long build up and they've reached the break through point. As you say, something September did maybe.

This show is good at raising questions. It's good at answering most of them, but definitely in it's own time.