Production -- last year Eli finished at QB15 per FBG ranking, a ranking which was lower than any time in his career previously. I beleive trying to work with a gimpy Nicks for most of the season and Hixon when Nicks could not go, plus trying to work with Martellus Bennett (who I really don't like as a pass catcher) for a season, plus Reuben Randle being a rookie, all contributed to that. Manning finished in the top 10 each of the previous three years (#6 in 2011) and with a healthy Nicks should be back in that area again. Ben finished 6 spots behind Eli in 2012, 6 spots behind Eli in 2011, and 7 spots behind Eli in 2010, and I see it as looking worse for Ben in 2013 while I see it maybe better for Eli with Nicks back healthy.
You can like Eli more if you want- I don't think it's unreasonable or indefensible- but this is weak sauce. Eli's overall rank is rarely low, but his PPG rank is usually junk. If you want to penalize Ben for never being on the field in the durability category, that's valid, but you can't double-count by penalizing him again in the performance category by using total points instead of points per game. It's like how QB rating double-counts completion percentage by using both comp% and YPA instead of the more sensible comp% and YPC (or ditching both entirely and just double-weighting YPA, instead).
Ben has outscored Eli in PPG in 5 of the last 7 seasons, and was within 0.15 PPG in a 6th. Most of the time, it hasn't even been close. Since 2006, among QBs with at least 32 games played, Roethlisberger is 8th in PPG (just behind Peyton Manning and Tony Romo), while Eli is 16th (just behind Jay Cutler and Andy Dalton). Eli averages 1.27 PPG fewer over that span, and that actually underestimates the difference because Ben has missed more games in recent seasons (in the more pass-happy environment) than early seasons, which causes those early seasons (in the less pass-happy environment) to be overrepresented in his average. And this is with Ben playing a lot more games injured and leaving a lot more games early. Ben Roethlisberger has topped 20 PPG in 4 of the last 6 seasons. Eli Manning has done it once in his entire career. There are a lot of reasons to prefer Eli over Ben, but the idea that he's been more productive when on the field is not one of them.
Eli Manning's PPG ranks since 2006- 18, 16, 18, 12, 12, 7, 17. 2011 looks a lot more like an outlier when you break it down this way. This is why I've always been hating on Eli Manning- he stays healthy and racks up respectable year-end rankings, but on a per game basis, he's going to get you slaughtered if you have to put him into the starting lineup.
Just for comparison's sake, here are Ben's PPG ranks since 2006- 9, 5, 20, 3, 7, 13, 11. That 20 sticks out like a sore thumb, but otherwise, Ben's second worst season (13th in PPG) is nearly identical to Eli's second best (12th in PPG), and Ben has four times as many top-10 finishes. Eli is much more durable, and has a style of play that should lend itself to a longer career. Eli has a dramatically better supporting cast around him. In terms of talent and history of production, though, Ben crushes him.