Aside of turning a franchise that's been ridden with losing seasons and mediocrity into a perennial contender. I'm not knocking Manning at all, but to slight what Brees has done with this franchise...
Actually the arcs are rather similar. In the 14 years after leaving Baltimore but before Manning's arrival, the Colts won 88 games (2-3 in playoffs). In the 14 seasons before Brees, the Saints won 97 games (1-2 in playoffs). Both teams went 3-13 the season before the QB in question arrived - and the Colts did it without a hurricane.
That said, Brees obviously has 3 years on Manning to compile a better career playoff record. And he'll need it to balance out Manning's stats, which are just gaudy. (Win a bar bet with this: Mark Brunell still has more career passing yards than Brees - at least until this October.)