Don
FEAR. The first one, haven't played enough of the 2nd one yet to see if I have the same opinion. FEAR is fantastic but I found it a bit long and got bored, so no, never completed it (yet).
Bioshock.. great game, appaling boss fight. I chucked a few RPGs at him, then wrench-jockeyed him to death.
I've played it through a few times, as I love the majority of the game, but the end boss was such a paint-by-numbers letdown.
KOTOR II was a prime example. You could see that the developers had their asses kicked half way through making the game. Dialouge was cut, planets & storylines/quests were cut and the general feeling of the game became slap dash. The last level was a complete joke, topped off by the most ridiculously anti-climatic ending i've ever seen!
Far Cry 2 : Ok, it lost its way after about halfway through the first area.
Most of the well known FPS games seem to start great then have terrible endings from Halflife to Stalker to Farcry and Crysis. In fact I'm struggling to think of one that had a decent one.