I don't understand the need for this eternal Manning vs. Brady debate. Two very different quarterbacks, styles and systems, supporting casts, playing environments and levels of experience.
I agree, there are far too many variable to consider.
Most writers and commentators are going by the "eyeball test" when they say Manning is better than Brady. They may haphazardly throw some stats in to support their argument, but these kind of statements almost always come down to gut reactions. That being said, if we are being honest with ourselves it is clear that this season Manning has played better than Brady. However, this does not mean that he is the better quarterback in the historical sense, which is the case that is being made.
The most obvious issue is that Manning has a huge advantage in terms of recent body of work. Brady did not play the 08 season and was coming back from a catastrophic injury in the 09 season. There is bound to be a major drop in performance during an absence like this, but it is rarely mentioned.
Even disregarding the recent history, there are so many differences to take into account that this question can never truly be an "apples to apples" comparison. Beyond the fact that you have a different supporting cast on defense for each player, the organizational structure around both is completely different. The Patriots have built teams with balance in mind, while the Colts consistently consider their offense first. Having Manning surrounded with the weapons he needs to be successful is clearly their number one priority.
The environmental factor has to be taken into play as well. Manning plays half his games every year inside a climate controlled dome, while Brady has to face the New England winter as each season goes on. Site whatever stats you like, playing inside the dome is the clear choice any quarterback would make to ensure they give their best performance. The benefits cannot be more apparent than they have been this year, as the Colts have hosted two teams in the playoffs who are built for cold weather football. Taking away one of the strengths of these teams gives the Colts, and by extension Manning, a huge advantage.
Another element which is disregarded by most commentators is the changes which took place within the NFL, namely the rule changes which have coincided with Manning's improved performance each year. In a decade in which offenses have played under what is essentially two different sets of rules, one which heavily favors the passing game, it becomes almost impossible to judge which player is better. Before the rule changes, Manning struggled heartily against quality defenses, namely the Patriots. Since the changes were made, he has steadily improved to where now he challenges pass defenses throughout the league. It is no coincidence that the rule changes were pushed through by parties with a vested interest in helping Manning perform better.
There are numerous other factors that one could list which make a tremendous difference in how each player has performed and which determine who is "better", however these are the ones which are immediately apparent. Commentators will of course continue to make these arguments, and fans will continue to take great offense at them. I'm not sure which is more pointless.
