While I admit the leather is nice, it just didn't work for me -- big dog (Doberman) with nails doesn't match with leather seats, even if there is a cover/blanket on the seats.
The NAV is nice, sure, but for $3400? No way -- I can read a map and I'll stick with them, for that kinda money!
The VDC is nice but I don't drive like a maniac, so it's not worth it to me.
Traction control. Do you REALLY need it with AWD? For me, it was no.
HID headlights are nice. Manually adjustable? Unless you plan on towing a lot, I don't think it's that useful.
Tire pressure monitoring system. Very nice.
Six-spoke alloy rims vs. five-spoke alloy rims. Big deal.
From what I've read on this site, the SE's ride is harsher than the SL's. For me, the comfort level is more important that the performance level, so the SL suspension suits me better.
I did, however, opt for a sunroof in my SL.
Keep in mind that the 04 SE comes with the manumatic gearbox (and only this gearbox, as I understand it.) For me, this is just a waste -- it turns what is a phenomenal tranny (the CVT) into essentially just another 5-speed. For me, the CVT was one of the things that attracted me to the vehicle.