Just to add to what I said before, but in less words, I think in Series 1 the show was going for an intellectual resolution. And somewhere along the way, the reins changed hands, or people realised that the intellectual resolution was going to require an insane amount of effort and plotting and balancing, and they ended up going for an emotional resolution. Which is fine but I'm an intellectual type of person so all the crying and warm fuzzies really wasn't up my street. I wanted hard answers to questions such as why was that Korean doctor's glass eye in that box way back in Season 1 and so on.
I hope that they will publish an official book companion which has "canon" explanations for all loose ends- it could even be written in response to fan sent questions so they know what boxes to tick- that it was not time/resource possible to get into the show. That way at least there will be a reference for the die-hard to tie everything up. The producers have said 20 mins was cut from the finale and some of that did explain more plot threads, but that may just be an ad for the dvd box set.