Doesn't matter if BCS, polls, new 'puter program, whatever, is used. One can make arguments for any two of these three teams being in the NC game. Without playoffs, the BCS is as good (or as bad) as any other system.
BTW, KRACH, which is argued to be better than RPI in hockey, would rate USC 7th, due primarily (I assume, I know little about any of the systems) to SOS. Believe the two ranked at the top by the BCS are the same two as KRACH.
Would seem that the only way a 'puter programer could get USC into this game would be to rate late season losses more important than early season losses, wide margin losses more important than narrowly losing, throwing out SOS (or making it less important), winning a conference vs. not winning, or combination of these and more.
Point is, there is no system that could be created that could properly place the right two teams (of these three) in the NC. Unless, of course, it's the system that places the two teams that YOU think should be in the NC.