Roethlisburger is a damn good QB, even if I hate the team, and I have no problem rating him or Eli above the rookies. Also, I think some of the rankings are a lifetime type thing, which is a disadvantage to new players. Eli Manning had a poor 2nd half of the season, but people aren't going to forget how amazing he's been in the postseason the last few years, and his SB wins....just like Big Ben had an off year(for him), but still put up good stats and played well.
Personally, I think they had Stafford ranked too low there. I also don't agree with Shaub and Ryan. Sure, they have great numbers, but right now, they aren't proven winners, at least Ryan isn't in the postseason. But then again, no rookie is a proven postseason winner yet either, so I guess it makes sense.
As for RGIII, Luck and Wilson, these are the arguments I've heard that make sense:
RGIII isn't asked to do as much. He has a 2 read passing offense, and runs a college offense. The SKins tailored his Baylor offense to ease his transition, so while he has production, he actually hasn't run much of an NFL offense.
Luck has been asked to do more. He has talent around him, has had to pass more to win games (thus upping his INT totals), and he's actually been handed the keys to the ENTIRE offense from day 1. He's been asked to do everything that Brady, Peyton Manning and Rodgers has, and he's handled it. He's making rookies around him better players, and he has as many rushing TD's as Wilson does believe it or not.
Wilson wasn't handed the keys to the offense right away, and there were some growing pains. I think a lot of his INT's were off the hands of his WRs, and while that has something to do with pass placement, I also think people completely disregard that fact and just claim he has more than RGIII. The national perception is that he started slowlly and grew into the player he is, while Griffin was hot right away (going back to the college/pro argument here). The production and numbers are roughly the same between RGIII and Wilson, so it's become a toss up between the two.