Advantage of doing a clean Install of Mountain Lion?
Installing cleanly gives you the advantage that you will know if an error is due to the "as-shipped" condition of the software before you add your data and applications to the mix. The installation of a new OS is the primary time when people notice corruption of a filesystem or other hardware type errors since a machine can often keep running well with some little errors. But relinking all the kernel extensions and drivers and knowing that your accessories and applications will all take to a major new OS is a lot of change. Spending a little extra time up front can help isolate issues if you have them.

By running the migration later, you have more control over things and can also choose to hand migrate anything first that you don't trust the tools to automate.