I've played every Madden since '91 and I have worked in the video game industry... so I know a bit about this game.
In my opinion PS3 Madden 07 is terrible from a gameplay perspective. Sure the graphics are higher resolution, but the animation is sub-par and the game isn't complete in all areas. For example you can't use custom button layout in all game modes. The responsiveness of the controls is very slow. I'm not talking about the controller layout but the precision of movement when you try to move your player around. I took the time to learn the new layout, which does have some benefits over previous versions, but the animation structure of the characters is difficult to control. To be fair, this is a trend in the PS2 version of Madden as well (each year seems a little worse), it's much worse in the PS3 version. An example of this is when you juke. You have to run through the whole juke animation before you can move into another animation. Since there are many animations that last many frames your players get stuck moving in ways that you don't want them to go. This makes the game experience hurkey jerky and unresponsive. It's frustrating to try and move a character and get no response. Sure, you can learn to account for the lack of responsiveness, but that's not football. The NFL is all about speed and this game just feels as though you're playing in a vat of molasses.
If you want to play online (by far the best game experience of Madden aside from friends on the couch), then it isn't even close which version to get. Online, The PS3 Madden experience is like playing the game with boxing gloves on. It's laggy and makes the game so unresponsive, it's pretty much unplayable. From what I hear, the 360 got a network code patch that fixed the issues on that platform, but I think there was a bug in the game in the network code for both versions. Maybe EA will patch, but I highly doubt it since the end of football season is almost here.
Lastly, if you do get the PS2 version, you will need to put your PS3 in a DMZ on your network to avoid connectivity issues online. I lost about 20 games with disconnects before I remembered that I had to keep my PS2 in the DMZ for the last few Maddens. Also, if you get a error that says No adaptor present keep trying. For some reason it takes a few tries to get through every once in a while.