That's the problem - Madden has a very limited set of attributes to affect the outcome of every play, and every player in the Madden universe is treated fairly, and progresses steadily with extended playing time, regardless of actual talent and intellect. There's no room in Madden for random and rapid progression or regression, or for any "intangibles." Sure, they've tried to address this with the "Roles" - they say if you have a "mentor" on the field, younger players at that position will play better, but has anyone noticed? I've tried signing such players specifically to try to speed up the development of young players, but there's no noticible difference in the youngsters' performance with a so-called "mentor" present vs. without him there. In real life, the presence of 1 player can make a huge difference (see the Colts defense with and without Bob Sanders playing). That doesn't happen in Madden.
Madden refuses to acknowledge that some players, no matter how much they play, no matter how many times they touch the ball, they simply will not become superstars (Matt Leinart, Ryan Leaf, Tim Couch, KiJana Carter, etc). It also refuses to acknowledge that sometimes, players drafted late, or discarded by other teams DO become superstars (Marques Colston, James Harrison, or Ryan Grant, anyone?). Heck, there's not even an option for a practice squad, or for players to come out of retirement (or be talked out of retiring).
It's telling that when you switch difficulty levels from All-Pro to All-Madden (at least on my PS2 console), the CPU doesn't play smarter - it just plays faster and surer. It catches balls that it may have dropped in All-Pro. Slow TEs outrun human-controlled speedster CBs, turning 5-yard dump-offs into 60-yard TDs. Scat backs shed 300-pound tacklers in the backfield to turn a 2-yard loss into a 20-yard gain. This is not how things should be. A player who runs a 4.25 should always outrun one who runs a 4.7 in a footrace, regardless of the difficulty setting. The difference should be in the schemes, the ability of the defenders to read routes and get into position to make a play, or for QBs to read defenses and find an open receiver. On All-Madden, a CPU QB should go through his progression and find the open man, not shrug off a 350-pound DT, then thread the needle into triple coverage to a backup WR who plucks the ball out of a defender's hands, spins and jukes out of the crowd, and outruns the field on his way to a score. But EA/Tiburon, et al would rather make the simple across-the-board ratings boost instead of actually doing the hard work of creating a complex AI system.
That's the root problem for most, if not all, of the shortcomings of Madden's gameplay, including QBs who throw 50-yard strikes across their bodies on a dead run.