I think what you're reacting to (and the basis of your whole disillusionment) is the fact that Staubach always *looked* heroic, even when he was very pedestrian (and he had plenty of those games in his career) and conversely, Eli looks like a jerky little kid who got his dog kicked.
But take that out and match up accomplishments ... and Eli is the superior QB in my mind. Most especially when you consider that he'll play for another 5-8 years (longevity being a big part of legacy).
whether you saw some of the past greats is one thing but in the last 30 years all you've seen of the past greats are high light reels. No bad stuff, slumps, picks, fumbles, etc. However you get to see that from the current QBs on a week to week basis. You see it all....the good the bad and the ugly.
Eli has his ungly moments and maybe more then some current great QBs but his results overall are what matters.....
Measure Twice......Cut Once"