Power: The 03-04 actually has a little bit more power, but I believe it is a heavier car.
Acceleration: Again, you are sacrificing power for weight... should be about even. The Y34's use a 3.13:1 axle ratio (which is low, they should have went 3.40'ish for better acceleration - I know a lot of guys have swapped gears from the 300ZX) but they did it for fuel economy. The 06's have a slightly shorter ratio, however are about a second lower... has to be the shift points, I don't know...
Transmission: The F50 cars have a much better transmission, but are geared for top end power versus low end and mid-range grunt like the Y34's.
Smoothness: The Y34's use a pretty archaic musclecar-type gear setup, so first and second are VERY tall gears, thus shift much harder. The 06's are all about being silky, thus giving up acceleration.
Handling: 2006, hands down. No numbers on 03 G loads, however the 06 went through a 600 ft slalom about 2 mph faster. Bigger tires certainly doesn't hurt either.
Fit and Finish: I might be crazy on this one, but I'm gonna vote for the Y34 here. I think the wood in the F50's look tacky and fake. I like the subtle finishes of the Y34, although it's not as big inside, I like it better.
Braking: Believe it or not, Y34. It's about 300 lbs. lighter, with the same size brakes.
Appearance: I have to go with the Y34 again. It stands out. It looks like NOTHING else on the road. It looks like something out of Judge Dredd, especially in black. The F50's look like a glorified Nissan Maxima... in fact I often mistake the Maxima for the the new M45.
Reliability: I think this one will ultimately go to the F50. It's built with higher standards than the Y34, and on a platform that has been proven for years. The V8 motor still has some issues, but that's going to be true of any high-valve, high feature V8 in it's class. The VQ series V6 is consistently one of the best motors in the world, so if you're looking for reliability, buy a V6. Actually just get a G35 because us M owners will pass you anyway.
For a more direct comparison... check out these links...
03 M45 vs. 02 Lincoln LS V8http://
www.motortrend.com/road...rison/
06 M45 V8 vs. 06 Lexus LS430http://
www.motortrend.com/road....html
Both were by Motor Trend and with the same test equipment.