03suzuka...s2000

In my opinion, yes the S2000 is hard to improve on. Me myself have a Berk header/HFC, coupled with a t1r 70mm single Exhaust. And that made a feelable difference along with a better throttle responce. I think an intake is pointless unless your getting it for the sound of it or looks.
I thinks pullys would do the same thing as a lightened flywheel. Take stress off the engine so it rev's faster but not ad any hp. Maybe just a faster rev time...

Worthwile upgrade list: (IMO)
A 70mm single Exhaust (but thos are very loud)
Some type of 1 peice suspention like BC
Possibly intake if the sound is worth it to you
And a test pipe or a HFC if your a law abiding citizen. Lol
A hard top
And possibly header (not too much bang for your buck tho)
And some Lightweight wheels with sticky tires on them

mister x

The OP stated the goal was to "stand out ", OK mods certainly help in that regard. In terms of cost/benefit, and I define benefit as driving pleasure, bone stock is the best overall value in the case of the S. Mods cost money and involve compromise as earlier stated, if you can tolerate that, mod till it hurts.