My opinion of the season finale is mostly good, but a little mixed. I like how they're pushing the envelope in terms of having us wonder "what the heck just happened? And what does this mean for next season!?"
What I didn't like was how they handled the 'death' of a major character: it was a cop-out, plain and simple, on par with your typical Trek-style alternate reality plot device. I was, however, fully expecting something like this, so it wasn't a big surprise finding out they went this route, just a little disappointing.