Brees was better from 05 on, and had like 20 passes as a rookie in 01. Brees was better during his time.
A short period of productivity is a knock on a player, not a defense for them. Brees, Manning, Brady, all came out very close to McNabb, and they get compared to these players.
The era thing is a cop out. Let's say 6 QB's are better than him from 00-04, then 4 fall off and 4 different ones step up so 6 QB's are better than him from 05-09. He wasn't a top 3 QB during the era (behind the 2 that stayed ahead of him the whole time). He was never better than 7th best QB... you're trying to call him 3rd. That's the problem.