multiple endings — more like ending with variations; the core of it stays the same.
special agent protagonist — player is appointed a job similar to this somewhat early in the game, so this isn't true from the start.
nationalism — the protagonist and his higher ups are constantly trying to drive the cause of the Human Alliance, it's importance and how you're part of it is constantly hammered at you and occasionally you get to do the same for others.
unlikely sentients — Rachni, Geth to some degree (in mythos puts them on par with rogue A.I.), the plant creature, and some others
dialog-keywords / dialog-stance — some are full sentences but not actually what is said, generally these are only choices on what to discuss and how to respond (aggressively or calm negotiator style)