The multiple flashbacks combined with the time skip were a bit confusing. But I don't mind time skips to fast forward the story through uneventful parts.
Edit:
More precisely, time skip, flash backs and rewriting the storyline happening one after another was probably a little too much. Well, it did make me stop for a moment to wrap my head around what was going on. Not too long, mind you.
I haven't played the newest update yet, but if Afterchoices just showed us the results of our actions instead showing "default" scenes and then changing them later, would suffice for me. I don't think the game needs to spoon feed us.
I hope it won't turn into a Hollywood movie, that thinks it's audience is dumb.