I’ve had extremely bad FPS in that final scene as well. I played the whole game with maxed out settings on everything and v-sync on with a constant 60 FPS except for a few areas where it sometimes dropped to say 30 FPS. Even though not state-of-the-art, my Radeon HD 5800 should handle it pretty easily at 1680x1050, which it has for most of the game.
The only part where it was downright unplayable was the last scene where you wait for the Xen portal to be ready. The FPS there dropped to 5-10 FPS at most. I couldn’t aim to save my life. I had to go down the ladder and hide from everything until the portal was ready and I could simply make a run for it. It happened from the very moment the portal was fired up, and for me wasn’t affected by quicksave/load.
I thought I may be hitting a GPU limit. I eventually got to the point where every single graphics setting was on the lowest options (I didn’t even know “Bilinear” still existed for heaven’s sake!). But alas, the FPS did not improve one bit. It might have been a CPU-bound limitation, but my quad core Q9450 should be able to handle it.
Otherwise a fantastic mod. Keep up the good work!
EDIT: I just loaded the autosave from the start of that scene and it played okay. Weird.
