THere has to be a balance of both.
Rouge Galaxy: awesome gameplay to the extreme. That is how FFXII's battle system should have been. But then the story was god awful so it had to go back to the store :(
Star Ocean Till The End of Time: Story was good.....all the way to the twist ending >:( Then it turned to crap!!! Combat was the redeeming factor. Seeing as 2/3rds of the story was good and that the battle system was on point, i deemed this one a keeper.
Magna Carta: Epic, thought provoking story, god awful battle system. I tried my hardest to tolerate it but when I got to the point where I had ran out of Element Mana or whatever it was called that game was beyond playable. Don't forget the fact that the battle system plays out like Star Oceans except the other characters dont move while you do. It almost feels like the game was incomplete.
Radiata Stories: Terrible everything except art design.
Final Fantasy 7,8,9,10,11,12; Persona 3,4;Kingdom Hearts 1,2: well balanced games that never utterly disappointed me. These are keepers :)