Mh...there're a couple of serious bugs:
-In Adytum after you brought weapons to the Blades, if you accept to help them in fighting against the Regulators the screen turns black.
-If you take the Holodisk to the Master and you convince him that the Mutants are sterile, he says you to leave and then you should be able to run away...instead the dialogue starts again in an unlimited loop and the only way to finish it is to kiill the master.
-It was probably already reported by an other user, but you can't push your companions away (as in F2) if they stop you in front of a door/passage.
-In Necropolis if you kill all mutants as required by Seth, he doesn't recognizes that you completed the quest.
-In the Military base,after killing the Lieutenant, the countdown for the base destruction doesn't start. It's necessary to destroy the base with the "diplomatic way" starting the countdown with the computers.
-During the end sequence the narattor tells that the Khang raiders are still alive and pillage the wastelands (although i killed them all in their base).