i just sold my 02 900 sport to buy an 00 996 mono.
they're not comprable bikes, at all; the ss is higher, softer, more comfortable and simpler. it's a great commuter and it's a great all around bike. i loved how simple the SS was and how (once you got the fairings off) accessible everything is in the engine bay; the only nuisance is the removal of the rear shock to do valve adjustments, but hey, whatever.
my ss was pretty much stock w/ the exception of termi slipons, and 998 forks. it did well on track, handled great and worked well but it was and is a compromise; where the ss starts to run out of steam at 110 the 996 is just waking up.
for me, the decision was based on numbers and what i'd spend to bring the ss up to the spec i wanted; i quickly realized that i'd be better off buying a sbk rather than converting an ss into a ss-sbk hybrid.
in my mind, the bikes are so different that it would be an almost fallacious comparison; both are great bikes but they're aimed for different purposes - i couldn't imagine daily commuting on the sbk (while you could) and i couldn't bring myself to spend the money to make the ss as quick and track ready as a sbk.
it really depends on what you want but in my opinion, if you're just looking for more power then that's the wrong reason to switch because while the sbk has more power, it also comes with its own character and it only really makes sense if you need a whole new package.