Another vote for Bionic Commando
My heart goes out to the team at Grin that gave Bionic Commando fans a brilliant 3D representation of the mechanics of the 2D games and wound up with nothing but a shuttered studio for it.
That game was dragged over the coals by pro critics, I believe largely out of complete and total misinterpretation of what the game was trying to be (and succeeding at). In review after review I saw it either subtly or blatantly criticized for not being enough like or as good as other games that it looked like it might be trying to emulate.
Sure, I could fault any game for it not being what I WANT it to be, that doesn't make it a bad game or a poorly made one.
As far as the story is concerned, the Bionic Commando games were never known for having engrossing or well told stories and in the modern entry it seemed like they were trying to ape some of Kojima's wackier moments from the MGS series which simply didn't play well for some.
Personally I thought the gameplay was satisfying to the point where I wasn't about to dock any major points for storytelling issues.