M04's are usually faster. (Because they designed it to use the TL01 pinion gears. 17, 19, 21.) Although the internal gears are the same on the M03's and the M04's, that addition of the single tooth on the pinion makes a world of difference when running the Johnson silver can motor. Also, because TCS requires you to run a rear wheel drive body with the M04, and a front wheel drive M03, you can put larger diameter rear tires on the M04 and give it even more of a geared advantage.
M03's are usually easier to drive. They're front wheel drive, so they tend to push. They're also less tempermental to setup, as I've heard some M04 drivers saying how it's the first time they've got the push or over steer out of the M04's.
Your choice would also have to lean on what's going to be run at your nationals. From my understanding, Tamiya America is going to have two seperate classes at Nationals. One for the M04 and one for the M03.
The only real hopups for the cars, are berrings and shocks. We've been shiming out the gear diff's to a great effect. I'd say to start off with the M03L. Because you can easially remove the center piece, and make a standard M03. Yet you always have the option of putting the center piece back in to give it the long wheel base.