One of the best aspects of the show was the clever, bantering dialog, and there wasn't too much of that.
It was nice to see the story get (mostly) wrapped up, but I guess it just wasn't terribly satisfying, since I could see how much better it would have been if they'd had half a dozen more episodes to flesh it all out. So I feel like I'm being extra critical of it, not because it's not a good movie (it is) but because it wasn't the second season that it could have been.
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Book's character was totally wasted. We never ended up getting any backstory about him at all, and he had the potential to be pretty interesting.
The new Reavers origin story ("it was teh drugs!") was much less interesting than the old one ("space madness!") I also found them much less scary than in the series. The very first Reaver attack, on the bank-robbery planet, was really well done (mostly because you hardly saw any of them.) But after that, they just seemed like the Borg's slightly retarded cousin. And in the big, alegedly-climactic space battle, I couldn't tell whose ships were whose. (Sorry, Brian...)
I fully expected the sexbot to be a Buffybot. How could they pass that up!
The "secret radio station hidden on the other side of the Death Star Shaft in the basement" was just total fucking idiocy. Give me a break. That whole scene was intelligence-insulting and a waste of time.
Also, haven't I seen that endgame in another movie? Oh, yes. Hackers.