The Authority wins if, for no other reason, the Ultimates aren't really that competent, if you think about it.
They've really only had three big battles: against the Hulk (nearly lost); against the Skrulls (could've lost, if not for the Hulk); and against Magneto (got their asses handed to them). They also took on the "Ultimate Six," which was actually comprised of a group of second stringers plus Spiderman, and beat them, but not that handily.
