It is interesting that, sometimes, the creators of game engines can struggle finding the story that can match the vision of how it's all supposed to look.
Id has the problem. All their engines for as long as I can remember stood better as tech demos than compelling games (they could get away with it more back when there weren't any FPS games to compete against - Doom, Doom II, Quake, Quake II). We forget sometimes how much they almost owned that FPS market back in the day. But, of course, they didn't make the best games using their own engines (American Mcgee's Alice, if I recall, was a strong story with great use of the idtech 3 engine. Of course, all the MoH games and Call of Duty games used the idtech 3 engines, until they updated to idtech 4).
Epic had the problem with pretty much every iteration of the Unreal Engine. Although the story on the original Unreal was weak, it was freaking loooooong and that length made it tough to finish! Others have made better games using their engines (Deus Ex, Clive Barker's Undying, Bioshock, anyone?)
Add Crytek to the list of developers who don't make the best games using their engines.
Who is doing it right? I can think of Valve right now, but certainly I'm missing someone.