Gotta say I really disagree with it feeling "natural" at all by the end and where we are picking up now.
Here's what worked for me:
-The season 1 shift: Like you said, it drove home the stakes. It was painful and interesting all at the same time, and changed up the status quo while still feeling like the same show, with the same cast.
-Death of Stephen: Again, right on the money. He was the badass, and at least for me(and I suspect many others) a damn likable badass. It upped the stakes even more, and was balanced out by the end of the episode where it was suggested we might see him in some form or another again.
-Replacement guy for Stephen: I liked Stephen more, but this guy works. Makes sense, and feels different enough in the same role.
-Death of Cutter: Talk about balls! Love it. THIS is what feels unfinished to me. Everything he is working on, we the audience feel it building to something but never quite get there. There was that moment where he is about to say something, then says it can wait. And on and on. In two episodes they left more threads with this guy hanging than pretty much any other death in television history. It was sudden, tragic, unexpected, and awesome. He had so much left to do. And only a few episodes after the OTHER main character bites it!
This, sadly, is where things really fall apart for me. It's a shame, because up to this point it was really kicking ass. But all that good will is soon wasted.
What doesn't work:
-Jenny leaving right after this: After 3 major cast changes in as many episodes, they decide to throw on another one? Too much. Also, too weak and easy an out for the character. The show begins to feel unrecognizable because (the main) 3 out of the 5 leads are now gone, only the comic relief and supporting character remain.
-Retconning the possibility of Stephen(or Cutter's, for that matter) return: This was a huge slap in the face. While it can easily be done anyway, to have the writers come out and basically say, "Too bad, they're dead, move on and get over it" was really lame. One of the biggest aspects of the show was the relationship between Cutter and Stephen, and to have both of those characters gone and have the writers basically tell us not to expect them back in any way(in a multidimensional time travel show in which other dead characters already showed up again) was a huge bunch of bull.
Which brings me to the worst thing thus far...
-DANNY: **** this guy. What a tool. Nothing against the actor I suppose, I mean I liked him getting shot in the mouth in Kick Ass, but his character and the way he is introduced and then written is absolutely TERRIBLE. He was annoying in the season 3 opener(or was it the second episode?) when I thought he would only be a featured character in that one episode. And then to have him show back up an episode or two later, kind of walk in the building and start making decisions and have everyone just "go with it" because he's a "natural leader" or some garbage? Absolutely awful. The show buckled under so many main cast changes, and this was by far the worst. It made no sense and was poorly done to boot.
-Going on from where we were: So now that the new season is coming, we've lost the main bad guy(okay, girl), the team's awesome Boss character, as well as annoying Danny. So 3 MORE major cast are gone now. And so far no one seems to expect anyone departed to return.
I love dinosaurs so I'll still be watching, but the show is just making me sad at this point. It had some big balls- whether due to actors wanting out or just taking risky story decisions- but didn't really know how to follow up with all that madness. Here's hoping they can salvage it into something satisfying.
