Rather than debate which system is better, I thought I'd actually answer your question.
Firstly, EA's recent offerings are all pretty close on both systems. Madden, NCAA and NASCAR are all nearly identical in terms of performance.
However, that's painfully NOT the case with Head Coach 09. I originally ordered the CE on the PS3, as I wanted free online play, and the PS3's much simpler way of transferring non-official roster updates. But, I exchanges the PS3 version for the 360 version last night.
The PS3 version locks up frequently, usually during transitions from your "home" city to the displaying of the opponent's city for away games. And this isn't unique to my PS3, as I tried it in another system and had the same problem.
The biggest difference though is in performance. When simulating actions, the 360 outperforms the PS3 easily 3 to 1. This is REALLY noticeable if you are setting out to simulate a season. With the 360 it takes a while. But, with the PS3 it takes a LONG time.
There is also a hesitation when making a selection with the PS3 that doesn't exist with the 360. When I say selection, I mean any action on the clipboard. With the PS3, you make the selection, have a slight pause, and then see the next screen. With the 360, it's instantaneous.
The easiest difference to spot right away is the on-field performance during a game. The PS3 is choppy washed out, and has the ever present hesitation. With the 360, the on-field action is smooth and more graphically appealing.
Believe me, there is a BIG difference between the systems for this game. You'll be MUCH happier with the 360 version.
BTW, before anyone thinks I'm knocking the game, I love it. Other than glancing at Madden, I haven't played it, while I've played hours of Head Coach.