I hate to be that guy, but if you are already concerned with "grinding" Flashpoints, and skipping or losing your patience with the story elements, this honestly might not be the game for you.
I mean, Bioware has pretty much made flashpoints for people who played KOTOR and Mass Effect like 10 times over, just slightly changing their story choices. Now I am sure they want to appeal to a broad audience, but design wise they actually made a game that is not grind friendly and to be honest I don't think they really want players grinding flashpoints. But the option is there for the "I beat ME for the 10th time today" players.
My guess is that they only intended for most players to run it 3 or 4 times, and again, if you are already itching to hit the space bar on that second or third run you might need to look to invest in another MMO.
This sums it up I think. Don't understand why grinding is something people look forward to anyways. I think thats the worst part of mmo's