It would be a bad idea for the Americans to install him as leader as they did with Karzai, because Massoud was Tajik and so the Taliban could paint themselves as a Pashtun nationalist resistance. Of course, this is the Bush administration we're talking about, so they could easily put an incompetent like Paul Bremer in Kabul who would do just that.
This is the crux of it. The Northern Alliance was a significantly Tajik and Uzbek led organization, and Massoud as President would only enforce this. Now, he was probably the best that the Northern Alliance really had to offer, but it wasn't like he an infallible figure.
I do doubt how efficiently the Taliban could paint itself as Pashto nationalist. There's no way that Massoud could muck up the situation any worse than Karzai domestically (the military ratios...those are another matter), and I think that, at the better end of the spectrum, Massoud might be better at re-integrating the warlords into Afghan society.
Now, here's the real challenge. A number of sources on Massoud (IIRC) stated that, even if he was a leader, he didn't want to stay one (he was originally an engineer, and wanted to return to that field). So the question is, if he steps down/dies, who succeeds him?