The trouble with nominating Condoleezza Rice is that she will remind voters of Bush. While Bush has many die-hard supporters, he is a liability in a general election at this point. Beyond that, McCain is seen as very strong on national security on his own. What he needs is a running mate who is seen as strong on economics, is significantly younger than he is, and who can motivate the conservative voter base while McCain uses his "maverick" appeal to gain independent voters.
Mitt Romney would be a politically prudent choice. While there could be bad blood between them, McCain has overlooked Bush's less than clean campaigning in South Carolina in 2000 enough to be quite friendly. If Mr. Romney is interested in the position, it would not be a surprising ticket to see.
Ms. Rice would be an excellent choice in other circumstances, but considering McCain is the single most national security oriented candidate, he needs to cover a weaker point with a VP candidate.