I definitely think it does. NCAA had all sorts of odd things for years, like editing the body of RB's would turn their arms skinny. If you edited attributes of o-linemen in Xan's external editor o-linemen legs would turn skinny (from editing attribute values only!). Not only that stuff, but guys have done some serious editing, and made the game play entirely differently, and even animate differently (triggering new animations, gameplay looking more fluid, etc...).
I have to believe there is just a terrible fundamental technology base in Madden carried over cycle to cycle from who knows how far back.
I know NHL and FIFA get a decent amount of hate, but I really am amazed by some of the gameplay design elements, and simulation facets I can achieve on higher difficulties with all manual controls, no assists, and some slider adjustments.
Madden is better, no doubt, but we still see many of the same issues and mistakes reappear any given cycle.