First off, cool idea.
Second, VERY cool work, capa!!!
One of the toughest parts would just be getting agreement from others on who should be on the team.
Although I guess you just put all the greats on the team, and each person has the option of playing whoever they want. Do you want Peyton Manning or Johnny U to captain the Colts? Well, you have both, so it's up to you! (Sounds pretty cool to me)
The other hard part will be agreeing upon ratings. As capa discusses on his site, you can't really give a LB from a team in the 1940's or 1950's the same rating as Zach Thomas, because they're just a different breed. Defensive linemen are so much faster today than they were even 20 years ago. So that will make it tough to come up with a ratings system. I know for the Community Roster project we decided to use some NFL.com ratings for the rookies, but you don't really have anything like that to help with this. This may be the trickiest part of the whole plan really.
Lastly, you'll have to take into account some team/city changes, as well as player changes. For example, Baltimore. Do you use the Ravens players, Colts players from back in the day, or both? Where does Johnny U go? Baltimore or Indianapolis? Which team does Marshall Faulk go on - St. Louis or Indy? There won't be a ton of these, but enough that they should be considered.
I'm not trying to naysay, or say this shouldn't be done - in fact, I think it's a pretty awesome idea, and would love to be a part of it if/once it gets off the ground. Just pointing out some things that should be considered and agreed upon before people start making their teams.
What do you guys think?