Love both cars. S is smoother, quieter, has 2 screens for better nav display, and has more cargo space, so better for road trips. (In fact we are on a road trip now, in my wife's X, which she wishes was an S but her father can't bend to get in one).
The 3 is more efficient, a little easier to wash and park, and has awesome handling and steering feel so I prefer it around town.