I would love for Ian or someone to chime in on this, because I don't see any way that this is the same engine. No one in their right mind would port a PS2 engine over to the PS3... NG Madden is built from the ground up, it just has to be, I would be SHOCKED if it wasn't.
To suggest that PS2 Madden and PS3 Madden share the same engine tells me that you have not played enough PS2 Madden. These are two COMPLETELY different games, period.