Both are great cars but in totally different ways.
Torque vs no torque
2 seats vs 4 seats
2 doors vs 4 doors
turbo vs vtec
fwd vs rwd
convertible vs non
I enjoy driving both but my MS3 is way faster though and more comfortable for everyday driving. The S is used mainly for sunny weekend drives. I have a civic for everyday commute and the MS3 is my "speed" car.
Something I've noticed about the S2K as the design gets 'long in the tooth'. It's one of the few cars (IMO) that is timeless. The car doesn't (and probably won't ever) look as old as it is. Never really wanted one, but I do appreciate a good design when I see one.