I'm really starting to despise the way most games handle branching stories (consider this: Black Ops 2 has a lot more branching storyline than most other games this year.) - and I think that Far Cry 3 is one of the worst offenders. Basically, what the game demands you do at the end is take responsibility for the decision the game makes for you about halfway through the game (when Jason decides to stay). I normally don't like it, but it's usually the main character ending up in a situation where you end up somewhere because of other's decisions. Here, the decision is just meaningless. Meh, MEH! I say.
That said, I did feel a bit guilty for letting myself be fooled about Vaas' sister being sane. Of course she's going to be nuts. Everyone is nuts on Rook Island!
In the end, I'm going with the Citra end, because... while I don't think Liza deserved what she got, I think that Jason deserved everything he got. :P
Anyway, I think that Vaas is probably the best character I've been introduced this year. Despite it being spoiled in trailers (WHY!?), the "Did I ever tell you the definition of insanity?" section was excellent... And so was pretty much every other part he appeared in. So menacing! So awesome! Unfortunately, I think that Sam and Hoyt couldn't quite pick up the slack for Vaas, though Hoyt was pretty good.
On the other hand, getting the wingsuit just after Vaas died... also made the rest of the game so much more awesome. It's almost like the game turned into Just Cause 2 - giving you crazy levels of mobility... honestly pretty torn about the game. Overall pretty great, but the bad parts are pretty bad. It's kind of a shame they didn't go the Tyler Durden route... but, there we go.