I am a long time BMW owner and I've had the 335i, M3 Cab and recently was considering the M3 Sedan vs the S4. The other posts are correct, they are not the same animal. The M3 is a Formula 1 inspired custom designed machine. I realized that buying an S4 is like the AUDI AWD version of a 335i not an M3. After driving the S4, it's nice but not nearly as polished, smooth or balanced. Also, with the S4 you've got power going to those front wheels which produces a small amount of torque and a loss in steering feel.
I went with the M3. Best of luck, both cars are amazing.