Actually, my recollection is that Dukakis was a much more popular choice in the primaries than Hillary or Obama. He had a lot of support. And there were probably a lot of people thinking he had to choose Jesse Jackson to keep the black vote but, in the end, most blacks voted for Dukakis over Bush.
The thing you also have to remember is that, right or wrong, an Obama-Hillary ticket (or Hillary-Obama ticket) would have looked to some independents and moderates as "Affirmative Action in '08."
You'd have an inexperienced black guy and an only slightly more experienced woman who, let's be frank, got where she was by marrying well.
McCain also married well the 2nd time too. At some point they both did more than just marry well to get where they have.
