I didn't really mind all the snipers except for a few spots, but I agree that the final boss was ridiculously difficult for all the wrong reasons.
And they don't even give you any hint in regard to how to fight this guy--must kill everyone and destroy his boxes, only for him to run to a different part of the ship so you can do it again.
Other than that, it's probably tied with LBP for my favourite PS3 game. Hopefully Uncharted 2 (U2 ) will not have these issues.