I think the main reason Nemesis bugs me is that it's the last TNG movie. As their grand finale, it should really be a lot more than it is. I didn't mind it all that much in the theater, but after it became clear that there would be no more TNG, it bothers me knowing that NEM is the end.
And hell, no Trek movie has ever packed as emotional a punch as ST09 did. I was sobbing ten minutes into the movie with the destruction of the Kelvin the death of George Kirk. And then the movie shocked the hell out of me when they killed off Amanda! I was completely blown away.
Data died in NEM, and the most I could think was, "Well, good thing he downloaded his consciousness in B-4 earlier in the movie."