I would have voted for Brees in 2006 over Tomlinson, for much the same reasons as I'd have voted for Manning over Peterson in 2012.I thought Peyton and Brees were 1a and 1b in the MVP race in 2009, but otherwise I agree; I can't think of any other season where he had a strong case to be the MVP winner. Definitely seasons where he was in the conversation (like top 3-5), but he has never had a season where he should have been the clear-cut winner and was robbed.
I have Brees>Elway, but I'd argue they are both overrated. Career cumulative numbers are a terrible way to measure greatness, as are single season numbers of different eras. I wouldn't call either a top-10 QB of Super Bowl era, and probably not top-15 of all-time.