I own both games. Picking a favorite can be tough. After playing them both, they both piss you off because they point out eachother's weaknesses (they're both great though).

1. Gameplay physics: 2K5 +2
Madden-not really different than the SNES version. Lots of mericle catches.
2K5-very impressive. You can feel momentum, the players legs make the cuts. They will automatically twist and get around O linemen. If you throw a ball into double coverage, the hit of the D backs will make the receiver drop the ball most of the time. Very few rediculous catches.

2. Training: Madden +5
Madden-I love football 101 and training camp. These minigames are worth hours of fun in themselves. Brilliant!
2K5-Basic training is too basic and easy. The practice mode is pretty good and you can play as offense or defense. They also include 190+ page manual on controls, gameplay etc.

During play control: 2K5 +5
Madden-The hit stick is nice, but HB get stuck on O linemen way to easily. It's like they're both squares. If they don't quite pass by the tiniest margin you're stuck like you're on a hook. Also it's anti intuitive that sometimes run is A and other times it's B. Lastly, runners always hold the ball in their right hand instead of on the outside. So when you try to use a stiff arm on the left side, they have to switch the ball to the other hand first...which means nothing happens for 2 seconds. Really annoying. One good thing is that ability to control the nearest blocker or receiver with the right stick. Oh yeah, the punt returning is annoying as hell. If you don't take control of the return man before he catches the ball and call for a fair catch, you will fumble evertime if you get hit immediately. They should be smart enough to call a fair catch on their own if you're not controling them. Lastly, the CPU will control the QB automatically if you don't do anyting for a few seconds. This is really annoying...you're waiting for your 1 on 1 receiver to get deep, and all of a sudden your QB throws somewhere else.
2K5-It's annoying to have to tap A to run, I'd rather just press it. The lower the shoulder move is great (can't do that in Madden), also the right stick controls are cool (hurdle, juke left/right, stutter step, stop short) can't do any of that except juke in Madden.

Before the play controls: 2K5 +4
Madden: The audibles suck. You have to pick 5 plays in coaching mode, and you're stuck with those. So if you're trying to run the ball up the middle, and you notice that they're overprotecting the middle and a wide receiver has no coverage, you can't do anything about it. If you call one of your 5 audibles, the formation will change and the defense will change with it. You can't simply pick a different play from the same formation. There's no excuse for this. The hot routes are also harder to use. You can also only move one receiver. On defense, D backs are harder to control as well, but there are more options for the D line.
2K5: The audibles are intuitive and the way they should be. You can pick a different play from the same formation or you can pick a preselected play as in Madden. The hot routes are simple and intuitive. You can move multiple players. No bonus points here because all of this is obvious and what I expect.

Other: Madden +3
I don't play with franchise, etc so no scores there. Other than the above, Madden's cheerleaders are ugly, but the otherwise presentation is good, I like it better than 2k5. 2K5 does offer an option to equalize the teams regardless of their ranking, this is nice. Madden lets you pick different years for the same team. The Crib is pointless, no bonus for that. In general, it seems that it is too easy to throw the ball in Madden and too easy to run the ball in 2K5. You really have to make a good play to throw the ball in 2K5. You won't get any bullshit catches into double/triple coverage. This happens all the time in Madden. On the other hand, I've won games pounding the ball up the middle every play (on all-pro difficulty) in 2K5. In Madden, because you're HB gets caught on anything, it's much harder to run and much harder to brake tackles even with special moves. But you can often make the same pass play every time even when double covered. Overall, I think the AI adjusts to your patterns (running the same play alot) in Madden better than in 2K5.

So for me, 2K5 wins by 3 points. But my opinions are heavily influenced by the actual football gameplay, control, etc. I don't use the franchise mode, and I haven't played either games online.

I've played Madden just over 12 hours, I've played 2K5 (bought it first) probably 3 or 4 times that. I still play both regularly, and they are both worth buying.