The Arena Football League(coming up on the 30th anniversary)
The World Hockey Association
I mention these off leagues because they have one on the USFL(Small Potatoes) and one on the ABA(Spirits of St. Louis) and these leagues have a great story to tell, especially the WFL which is precisely how not to run a new football league. Other stories:
The athletes effected by the 1980 Olympic Boycott
Phi Slamma Jamma
The Wizard of Westwood
Bobby Knight
The 1964 Phillies
The 1980 Phillies(Just as intriguing a story as the 2004 Red Sox)
The Negro Leagues
The All American Girls Professional Baseball League
Ali vs Frazier
Appalachian State defeats Michigan
Army vs Navy
The inspirations for subjects is endless which is why I find it odd they felt the need to devote 2 episodes to Miami University.
And to piggy back on your idea of Brady/Manning, one on the Manning's in general would be good too.
March Sadness: A look at the late-70's to mid-80's DePaul hoops teams and their disappointments in the NCAA tournament.
Miracle In Manhattan: A story about Bill Snyder's turnaround of Kansas State football.
The James Gang: A story about the early-90's Washington Huskies football teams.
Wide Right: A look at the Miami-Florida State football rivalry from 1987-94 and 97-02.
Draftniks: A look at a cottage industry of NFL Draft enthusiasts that started with Pete and Carl Marasco's work in the late-60's. Would also cover ESPN and their televising of the draft over the years.
I'd love to see one on the Biggest upsets in Sports/Boxing history and that is 42-1 underdog James "Buster" Douglas vs. "Iron" Mike Tyson in Tokyo of 1990.
It's still, to this day, a monumental shocker. They could also delve into *why* there was never a rematch or something. It would put a new perspective onto things.
*That* would be great.
Others I can think of, without getting into why:
Michael Jordan's return after his *first* retirement. #45 Jersey and all.
A Pete Sampras. The last world #1 that America has produced. (Can't remember if Roddick was ever #1 though)
A real "Raging Bull". Jake LaMotta is still alive, believe it or not, and it would be great to hear about his life and career from the man himself.
Super Bowl III.
The '07 Patriots and how they almost went a perfect 18-0, but lost to New York in the Super Bowl.
Something on Nolan Ryan and his long, storied career.