I remember 2003. Flutie looked like an actual honest-to-goodness quarterback. Brees did not. With Flutie, the Chargers looked like an actual honest-to-goodness football team. With Brees, they didn't. Flutie was LIGHT YEARS better than Brees in 2003 despite playing with the exact same supporting cast.
"Light years" is an exaggeration. Flutie looked better because he could scramble to avoid the rush. It was a style of play that allowed an inferior team to be competitive with superior opponents, but it wasn't going to work in the long run and San Diego failed to see that.Brees is like Kurt Warner -- give him a good O-line and decent receivers, and he's the best in the league. But force him to scramble and he's mediocre at best.
Brees isn't a bad scrambler. And he did a good job even in 2003 of avoiding sacks. His sack percentage was higher than Flutie's, but still pretty good overall under the circumstances.The offense did fit Flutie better that season. The offensive line was horrible, and as a result, the Chargers generally kept extra guys in to block, often getting just two guys into the pattern. It was not a timing-based offense that spread the field and let the QB pick the open man (which is where Brees excels). It was waiting for David Boston to break open for an instant against a double team and having the QB rifle it in there before the window closed.Brees's arm strength has improved since his surgery. But when he was in San Diego, he was one of the weaker-armed QBs in the league. (Some people say that Philip Rivers has a weak arm. I watched the two of them side by side in practice quite a bit. Rivers had a much stronger arm than Brees in terms of zip.)So the offense at the time just did not fit Brees at all. It fit Flutie better. A lot of people thought Brees stunk back then. My view was, "How can we know? We haven't given him a chance yet." That's why I wanted to draft Robert Gallery.

But you also can't fault AJ Smith for taking a QB in 2004. For one thing, I think drafting for need is overrated, and Smith got the best player in the draft regardless of position. But even based on need, if I was right that it was impossible to know whether Brees was any good (since he hadn't really gotten a chance), then Smith was also right that the Chargers couldn't feel set at QB. Moreover, the competition from Rivers may have been a big factor in Brees's improvement.