I think what seperated Manning from Romo is playing on a more talented, and better coached team during his career.
Or a run game, a commitment to it, and a consistent Oline.
Over his career, the Giants' league rank in rush offense has been
[11, 6, 7, 4, 1, 17, 6, 32]. When you have a rushing offense like that much less is asked of you as a passer, especially when you're combining it with some of the defenses New York has trotted out over that period. I mean good grief Eli has had to play three seasons without a top 10 rushing offense, and only two without a rushing offense in the league's top half. There's a reason why you see those graphics about how great Eli's numbers off of play action are compared to non-PA. It's because he has been blessed with an effective running game scaring the defense.
Compare that to Romo, whose rushing offenses over his career have been
[13, 17, 21, 7, 16, 18]. He has only had a top 10 rushing game ONCE in his career and only had a rushing game in the top half of the league twice in six years. He has to carry the team on his arm, and he does it at a much higher level than Eli - consistently. If you are choosing a player to start a team with and you are smart, you would be more inclined to choose a QB like Romo or Brees or Peyton who has proved year after year that he can do it himself, unlike Eli who has not had to do that.
Last year Eli played out of his mind good. He had the worst run game in the league and carried the team with a 90+ rating, his performance against SF was awesome.