Just finished it, and my only real complaints came at the end. There were some silly jumping puzzles and you can end up completely fucked before the final area if you didn't use all of your money to buy ammo. Starting another playthrough with the mods suggested above and they certainly make a very positive difference (I also turned off weapon degradation so I don't have to worry about it anymore). Gotta say, I see why everyone speaks so highly of SS2. Great stuff!
wrt weapon degradation, I think modding Repair to slow degradation (I think maintenance does this already) passively would be interesting.
ADaoB actually seems to reduce weapon degradation a bit on its own. I haven't had anything break, but I remember, in the unmodded game, stuff would break fast.