Having the same concerns regarding Unity3D.
One could say Unity has it's limitations language wise. I understand the points argued against it and I'm in awe with anyone capable to program a 3D engine from scratch. The game industry certainly wants folks who can do this. Having no delusions of ever getting to that level any time soon, I continue to learn what I can and use all the bells and whistles Unity has in the meantime. It's just great to see fast results!
cheers! and best of luck on your game man!