I'd have to say that the story is most important for me, but fitting gameplay is almost equally important. If the inconsistencies between story and gameplay are too great then the game isn't all that fun for me, but I can forgive the annoying or weird bit here and there (SH2's combat system comes to mind... dear lord, a 3-legged kitten would have been more apt at using those melee weapons).
I am able to adapt/shift on this, too; for example, I can still enjoy a game like Just Cause 2 because every now and again it's simply fun to shut off your brain and start dicking around for a while.
Graphics are still important to me, but ultimately negligible if the other two factors carry enough weight. Nier, for example, was faaaaaaaar from today's graphical standards, but I still enjoyed it because the overall story and gameplay were simple, yet very entertaining.