Besides Pennington in the 1999 class were 3 QBs ahead of him in the Heisman voting: Hamilton (Sr), Vick (Fr), and Brees (Jr). Ratay (Sr) from La. Tech was #10. There were some other pretty good senior QBs that year too (Tom Brady, Chris Redman, Marc Bulger, Tee Martin, etc.). Pennington was drafted in the 1st round in 2000, everyone else went 3rd round or later that year.
I don't feel that just because you didn't make 1st string all-American you aren't HOF potential. To be named 1st string AA means you have to be recognized as the best QB in all Div I; competing against every QB in the country; freshman through senior. There is also a bias against anyone from the lower conferences being a 1st string AA. If you look at Pennington's value to the Herd and his stats he definitely deserves HOF recognition. Ask any Herd fan who the top 3 QBs in Marshall history are and Pennington will be mentioned every time - usually at #1. As good as Michael Payton was (and he was outstanding), many would not put him in the top 3. But since he was the IAA version of the Heisman winner and 1st team IAA all-American he qualifies and will deservingly enter the CFB HOF.
If you read the HOF criteria you will see that Moss may have a problem too because they place some weight to getting a diploma and staying out of trouble.