The problem with the PS3 analog layout is that your left thumb is almost always on the stick. The placement is more natural on the 360 controller. Having owned both systems for so long, you'd be crazy in thinking the PS3 stick layout was comparable or better than the 360 layout.
The right analog being on the bottom half is perfect, because you are constantly switching between the buttons and the stick. Also many games won't even utilize the right stick all that much, wbile the left stick is always used.
I will always prefer the 360 layout, but the PS layout is still functional.
My right thumb never leaves the right thumb stick for longer than 1/5th of a second. My left thumb never leaves the left stick, either. The muscles on my thumbs say that to keep them pointing upward, like you have to do with the xbox, is actually moving a muscle. If I let my thumbs go limp, they point outward, and actually end up resting right over the playstation analog sticks.
I still find it weird everyone else's thumbs DON'T do this...