Number of TDs Brady threw in his first Super Bowl season: 18
Number of interceptions as a percentage of pass attempts for Tom Brady in his 50 touchdown season: 1.4
Number of interceptions as a percentage of pass attempts for Alex Smith this last season: 1.1
Thus, Alex Smith was better at throwing passes that weren't intercepted than Brady was in his record breaking 50 touchdown season. /youfail.
More, you're comparing a Hall of Famer with an above average passer.
As for Manning, if he went to the 49ers, they would instantly be the best team in football, assuming he was healthy. This was a 13-3 team that got there with a game manager as a QB. Imagine them with one of the top 5 or 6 QBs in the league? (oh, and considering the talent on this 49er team outside of the QB position now that they have Mario Manningham and Randy Moss added to Vernon Davis, Frank Gore, Delanie Walker, Michael Crabtree on offense and the best NFC defense, he may leapfrog from one of the best to THE best- Manning has never been on a team as talented as San Francisco).
I see 14-2 as a very good possibility, and a sixth Lombardi trophy should he end up in San Francisco and be at least 80% of what he was prior to the surgeries.
... but of course, the reality is that this is all a price-fixing ploy by Manning, Smith, and their agent (they share an agent). Manning flirts with San Francisco, so Denver will have to increase their offer, meanwhile Alex Smith flirts with Miami, so when Manning signs with Denver, the 49ers will come running back with a fatter offer to stop him from becoming a Dolphin. It is brilliant.