ST still has quite a few code issues which have yet to be fixed. It also lacks polish in several key areas. The dots aren't the best and quite frankly suck compared to the LCD on SW. But, having said that I would say ST is the better shooting game. Combos on ST flow nicely whereas on SW not so much. SW also overwhelms with perhaps too many multiballs which can make 4th level missions a bit more tedious than fun.
I sold my ST because I hated the lack of polish the code had. Animations with no sound, bugs in nero 2 still, broken pop values, lack of black hole values and the less than stellar away team implementation. It also still has a game crashing bug which Stern knows about, but have not released a fix in almost 2 years.