I agree. First off, Madden 09 is not perfect by ANY means, but I have All Pro Football, as well as NFL 2k5. They're basically the same game, except one has the NFL license. So anyway, when I first got APF, it just wasn't that fun to me (maybe due to the generic teams).
Fast forward, I get my first Madden game since 2002, and its ok, but I'm thinking I liked NFL 2k5 better. Mind you, APF has the same gameplay as NFL 2k5. I pop in APF, and it still wasn't that fun to me. Then I realized...what made the 2k series better was the presentation. I'm not just talking about commentary or the halftime show.
-menus were organized better, especially during play calling
-they had sliders, multiple camera angles
-little things like real time injuries, and coaches reactions to when a challenge is called (yes, they show both coaches on the screen as the ref makes the decision.
-you actually see the ref throw out the flag, instead of PENALTY popping up on the screen.
APF/NFL 2k5 had more realistic animations, and a better flow of the game, but it played kinda stiff. Madden has unrealistic animations (doing a spin move at full speed to catch a ball, QB jumping in the air off his backfoot to make the perfect pass, etc...), but at the same time, it feels like I'm more in control.