Unless you absolutely need to dump it, keep the S2000. One of the most special cars ever made in recent history. Agree with the supercharger suggestions if you feel it's too slow.
It's the reason I'll never get rid of my V8 R8. High strung/revving N/A cars with a manual transmission are where it's at. Doesn't need to be the fastest car on the street, but nothing else gives you the experience of revving to the moon (in my case, 8500 RPM) with a manual.
When I first got my M3, I sort of neglected the R8 for a while. Took it out about once a month to get the fluids and tires moving. But after the new experience of the M3 wore off ~2.5 years later, I find myself going back to the R8 a lot more even though the M3 will blow the doors off of it. Don't get me wrong, M3 is also a fantastic car, but turbocharged engines are so ubiquitous now that they're all starting to feel the same. Getting into the R8 brings me back to a time where sports cars were focused more on passion and soul, and less so about meeting gas mileage requirements.
You'll get back to loving the S2000, just give it time. If you can afford to keep it, better than regretting selling it later. E46 M3 is also a fun car, but I think you'll have the same feelings you do now, just with more headaches
.