The biggest problem with this is that a large portion of the 2008 primary was shaped by Iraq. One of the many reasons Clinton had/has trouble with the Left is her vote in favor of Iraq, while in 2008 Obama was able to point out that at the time he had spoken publicly against the Iraq War. So on the major issue of the Democratic Primary, simply put Obama was right and Clinton was wrong, and Clinton has never really been ever able to figure out how to get out from under that.
Additionally, let's not forget that frankly Clinton's '08 campaign was laughably incompetent, such that merely being mediocre last year constituted massive improvement. Her staff were constantly at war with each other (i.e. Patti Solis Doyle and Mark Penn, as campaign manager and chief strategist respectively had veto power over hiring choices, and they hated each others guts, also Clinton constantly avoided stepping into her staff's disputes to make decisions), their strategic sense and ability to control spending was near nonexistent (they burned through $100 million by Super Tuesday thinking that it would be a knockout blow, supposedly in no small part because Penn thought that delegates would be awarded on a winner take all basis), and on so many things were utterly tone deaf (Clinton tried to get Caroline Kennedy, who was leaning towards supporting Obama, to campaign for her by having a staff member ask her, and of course Bill told Ted Kennedy that "Obama would be carrying our bags a few years ago, and Bill's general conduct throughout the campaign as a whole). Obama by contrast ran a far smoother and far more competent operation than Clinton did in 2008, and was able to win the nomination and the Presidency twice not just on his personality but also on having finely tuned campaign apparatuses behind him.
Even with the just the latter factor at play, my sense is that any permutation of Obama v. Hillary will end up with Obama winning 9 times out of 10 based simply on Clinton's demonstrable ineptitude and incompetence. But a Presidential race of course has so many elements that are contingent that by changing so much of recent American history you'd end up with a campaign that would be wholly unrecognizable.