I'd say the M3 is probably more comfortable as a DD, but that's a bit subjective.
The cost of using a E46 M3 as a DD these days is awfully high though. I currently commute ~80 miles a day, and have just about ruled out the E46 for that reason alone. The VANOS issues, the valve adjustments every 15-20k, the cost for general consumables (7-8 qts. of 10W60, brakes, etc.)... absolutely amazing car, but man, can they run up the $$$.
Congrats on the FR-S, sounds like you'll really enjoy your time with it.
