Leaf was immature, and Manning had the coolest head, for sure. Leaf was primarily responsible for his own undoing.
However, the Colts as an organization had their act together very nicely.
Indianapolis had a much better framework in place, while San Diego kept pissing away high draft picks.
When you have supporting cast the likes of Edgerrin James, Marvin Harrison, and later, Reggie Wayne, your QB is going to have a much better time of things.
San Diego didn't have nearly the same offensive weapons. The only area where I'd even say they were comparable was at the TE position, where Freddie Jones was a very good TE for them. Natrone Means was hobbled, and in the twilight of his fading career.
The fiasco with Mikhael Ricks was probably the worst. They gave up a future 1st round pick to select him in the 2nd round of that draft, and he never became that big time WR1 they were hoping he'd be. He finally hit his stride after being converted to TE, though, but that was after he left the Chargers
I don't dispute that Manning was the better player overall, but I do sometimes wonder what would have happened, if Leaf had gone to the Colts instead, where they had superior QB coaching, better talent, etc.