pause is to let you stop the action in the middle of a turn. when you hit the next turn button, a lot of things may be going on and esp. if your computer is slower, you might have to wait through a lot of messages and action, depending on your game settings.
pause literally interupts everything so you can walk away from your computer or whatever if you suddenly need to leave. I never use it and it's probably overkill, but there you have it.