I'll repeat my response to the Codex review from another forum:
That is the design, long stretches of combat followed by a few decisions, which usually only come at the end and thus don't affect the quest itself, the quest itself being the long stretch of clearing out rooms.
Edit: What I'm trying to say is the filler combat is not an accident, but endemic to the design methodology, an MMO trying to masquerade as a single player game by providing a few "meaningful decisions". Though perhaps not immediately obvious, Mass Effect tried to do the same thing, only not as well.