I think it's almost pointless to compare a 3D combat game to a 2D game. They're just too different. People who are more 2D RTS-oriented will prefer GB, people who don't play 2D RTSes will prefer FC.
I personally don't play 2D RTSes because of the grapical quality. I would hope that the gameplay of GB would be better than FC but I thought the "in-your-face" 3D combat of FC was awesome. So really, I'll never be able to make a comparison between the two.