This is a good show and I've been watching from the beginning but I can't help but think the writers just left earlier storylines unresolved as the show progressed and they focused on this multiple dimensions thing.Warning: Spoiler! (Click to show)
For example, I don't think they ever answered what the deal was with Olivia's former partner (boyfriend?). Wasn't he involved in some of the "fringe" stuff happening in the beginning?
I mean, if the entire point was Walternate trying to protect his universe then we can pretty much just ignore the first 2ish seasons or so.