I have no problem with end bosses. The boss fight in The Witcher 2 felt very weak and disconnected because of how out of touch the main villian was throughout most of the game. Far-away villians like in LOTR touch base with the reader/player as an ominous presence throughout the story to ground the reader/player in the plight they are facing. He was introduced and then kind of petered out until the very end. Didn't feel like it had much weight to it, which is my main complaint with the story. Even after defeating him, it was almost as if Geralt simply shrugged, walked off, and the credits rolled.
Part of my issues is that the developers seemed to think they needed a boss fight precisely because it is expected (to your first point) and had to stage, what I felt, was a unsatisfactory final encounter or they did not properly build to it. I'm sure you could go plot point by plot point and try to explain why Letho was properly built and so forth, but, for me, it simply did not leave a lasting impression.
I still really enjoyed the game, I don't rank the story high on my list though. :thumbsup: