Every time I start looking at modifications I come to the conclusion there isn't much to make the car more fun. Let me explain:

Suspension: CR suspension is already awesome. You may be able to tweak faster times out of some high-dollar suspension but it won't be much. Lowering helps the looks but hurts the handling.
Motor: You aren't going to be making much more power out of the motor (if any) due to standard mods. Turbo would make it more fun but also costs an enormous amount to do correctly ($8k for turbo kit, $3K+ for diff/axles, clutch, larger radiator). With that ammount of money I can go get a really nice sportbike or a good boat and have more fun.
Exhaust: Only s2000's I've heard that sound good are the "UK mod" ones, I hate the annoyingly loud/raspy ones.

The only things I can come up with are maybe a diff ratio change, and I wish i could find a way to improve steering feel (maybe with a manual rack) but I haven't seen any comments on that.

Fun for me comes from the feedback the car gives you, any ideas on how to improve that?

 

May people have proven the s2000 stock suspension is fantastic...
Superchargers seem to do pretty well, especially science of speed, which can make pretty great linear power out of a BONE STOCK motor, you don't need all the drive train work other than a clutch, which is a wear item anyway and would eventually have to be replaced.
Cooling system works perfectly. and out exhaust system flows pretty well for its size...
If you want "more fun" SC it. the base SOS kit comes completely plug and play all you have to do is tweak the fuel ratios.

 

If you have a CR, then I think you would definitely have more "fun" after installing a Gern-Pipe and a custom FlashPro tune. It's a totally different car when you have 10% more torque in the midrange!

 

I hear some pretty mixed feelings on superchargers. All top end and very little extra mid-range. Wish the SOT was still out there.
I actually have an AP1, but will be installing CR suspension, for tuning still need $1.5k for fairly small hp gains.
I considered a V8 swap, however I am not a fan of cutting structural members that will make the chassis more flexy.
Hard to improve the car when it's already so good!

 

Only big change to fun factor I have done is the supercharger. Night and day difference. Insanely fun to drive now! The car is just painfully slow NA imo. At 400whp it feels really well rounded now. Has the power to back up the looks, handling and feel. I plan to up it a little more but I could never go back to NA with this unless using it entirely as a track car.
It's true the sc powerband doesn't add a ton of midrange like turbo. But I am making around 230whp by 6k. More than an NA s2000 will put down at peak power.. So there are certainly still some mid range gains with a sc kit. At 9k I'm making 406whp.

 

Nice!

 

I dont think you will find any one item that will change the car as much as you want. Personally, Ive added suspension, tires, exhaust, shift knob, and an aftermarket seat. Each one of them didnt seem to make a huge difference but after driving a bone stock s2k for comparison I am very happy I did it all.

 

I find it absolutely hilarious you feel a supercharger or turbocharger is too expensive for power, yet feel a LS swap is a viable option? You seem all over the place. For the price, FlashPro is a fantastic addition to the car, and DEFINITELY makes the car more fun.

I also feel you've grossly exaggerated the pricing on a turbocharger. Supercharger kit maybe - but I'm at 350whp and don't have upgraded differential, axles, driveshaft, etc and have no issues.

 

This isn't exactly on topic, but the proper wheel/tire set up absolutely makes the car. This is an extreme example, but one that applies to many. If you go from stock ap1 wheels/tires to 17x9s all the way around w/ RS3s or Star Specs it's a COMPLETELY different car. But sometimes driving around on those stock ap1 wheels can actually be more fun.

 

You can add a 6-7 psi supercharger good for around 300 whp for $3-4k buying used. I didn't even need the clutch upgrade.