On the same token if you adjust for the statistical increase in domes you have to adjust for the statistical decrease in outside games late in the year for a QB (and team) that is conditioned to play inside. Brady absolutely has an advantage in the elements because he plays in NE.
I'd agree with that, and I do think it gives Brady an advantage, but not statistically. And so much of the Manning over Brady discussion revolves around statistics.
If we look at Manning from 1999 to 2001 (excluding his trial-by-fire rookie season), his completion percentage was 62.4%. I chose this period simply because he was in the AFC East, with road games to Buffalo, NE, and New York. Once moving to the nicer AFC South, his completion percentage rose to 66.8%. Part of that was his maturation as a passer, no doubt. But conditions also play a part, and that shows even in the past few years with Manning at his peak.
2009 was a great season for the Colts, but overlooked was the fact that 10 games were in domes, with 4 additional games in cities with traditional good-weather. The only games in traditional cold-weather cities were Baltimore in week 11 (45 degrees, mild wind, sunny) which was a tight 17-15 win, and the last game they didn't bother with against the Bills.
2008 was Manning's recovery year so hard to say much. But the only cold-weather game he played this season was against the 4-12 Browns, a 10-6 win where he threw for 125 yards and 2 INTs vs. 0 TDs.
In 2007, they dominated a 5-11 Ravens team in the cold. The rest were warm-weather/dome games. The only other game that kind of fit bad weather would be Carolina in late October, a big win where Manning completed only 46% of his passes.
A lot has also been made of Manning rebounding from some disastrous playoff statistics. But it's also worth noting that this has happened when the Colts have won enough to secure home-field advantage, or play in warmer weather. Since 2006, Manning has gone 6-3 in the play-offs. No surprise that only 2 of those games were on the road, and only 1 was in cold weather (Baltimore).
So the conditions do have some impact on the statistical edges Manning has currently.