deleted_user: Are you playing the GOG version? I remember those issues from waaaaaay back in the day, but when I play now everything is bright and easy to see. I'm thinking DDFix and possibly the texture patch helped solve those issues. The GOG version has DDfix and the mods page lists the texture update among other things.
As for the last mission... its my least favorite, since its HUGE and the only one that really enforces backtracking... but still worth finishing if you made it that far ;)
Yeah I'm playing the GOG version(s). I read the originals (without 3rd party fixes) had a problem for many where the ingame gamma settings didn't work at all. For me they seem to work (GOG versions), but on some levels and some places I still have problems seeing much, even if I have the gamma settings at full and laptop screen brightness at max. It also depends on how bright the room is where I am playing (reflections from the screen etc.), so playing in a dark room helps too.
Playing on the LED TV works better, but also there I need to set TV's gamma settings near to full. But then at least I'm able to see better also in the dark sections of levels.
I think the level where you were following a messenger was one of the worst, it felt I couldn't see shit most of the time.
Interesting that the last mission would be the least favorite for you, as some Thief 2 Wiki page lists it as "arguably the best Thief 2 mission". :) The atmosphere is great with the speeches from the speakers etc., but those robot spiders are super-annoying. For the bigger mechs, I feel I've already destroyed like a dozen of them one by one, but still I face more. :) If I see a lonely mech, I try to disable and destroy it without using any water arrows (trying to approach from the back, and blackjack it 18 times to disable, and a few more times to properly destroy it).