I like the idea and there's clearly been a lot of effort put into creating this, but I think there's a reason that Pro Bowl selections are voted on in the NFL and not based on just stats: stats can't determine completely a player's impact on the game. For example, how can you measure Champ Bailey's impact on the passing game when he only gets thrown at a few times a game? Or is it really more impressive for Robert Mathis to have more sacks than Dwight Freeney even though Freeney often gets double-teamed?
I think that the way that offenses and defenses are set up will affect the stats that a player has. Some teams like to blitz safeties, which will give those safeties a boost in hurries and sacks. Other teams like to keep the safeties back in a cover 2, maybe giving them more PDs. Still other teams use their safeties on TEs, meaning more PDs if the opposition uses their TEs, fewer if not. The same applies to CBs based on whether a team plays man or zone. On the offensive side, for example, if a team chooses to throw away from a CB, then the WR won't accumulate stellar stats for that game.
As for the argument that using only conference stats evens things out, I'm not sure that it does. In each conference, there are bound to be teams that consistently lose by unheard of margins, but the way that they are beat inflates different players' stats. Some teams choose to run almost exclusively while others choose to pass almost exclusively - both cases resulting in stat inflation. How can you account for this type of stat inflation? And maybe more importantly, are you choosing the BEST players if stats can be inflated over the course of a season?
Is there a way to incorporate team strategies and opponent matchups into the Pro Bowl formula? It's a great idea and I think there's clear support for it, but there's a reason that in the NFL players are voted on by the fans AND the coaches.