I don't think comparing it to used or modified cars is very fair. I understand what you mean, though, and yes, the S2000 isn't that impressive anymore. Still, its straight line acceleration is very respectable for what it cost at the time, even when adjusting for inflation and average power isn't the only thing that went up, weight did too.
What can you get that trounces it for the price? Even a Golf GTI doesn't do much better (and you can't even get it in manual anymore).
I'm comparing it to used cars because it's a used car nowadays and because people don't drive exclusively new cars (which sets their expectation for acceleration) and because old cars are often so cheap you can't even get a Sandero for the price. I don't know how much an S2K costs now used but last I checked non molested ones were essentially collector items. They were in the nice Porsche Boxster territory. That was corona midlife crysis market though.
I looked up the price of the S2k new, apparently MSRP was ~32k$ for the AP1, inflation adjusted ~55k$. It's quite a bit. You can get a B58 Supra, M240 (again B58) or like an S3/TypeR. The S3 doesn't have a manual but the others do.
The Supra is probably the closest because RWD and it's an available in manual, 4s car with a B58 if eventually potentially you want to make stupid power in the future. Much heavier than the S2K but only the Miata and exotics exist in the lightweight convertible/coupe space nowadays. You do get an IMO lexusesque interior though.
Last minute thoughts:
Maybe a Caterham but then you're getting into stupid impractical territory.
Oh, actually the BRZ/GR86/etc is pretty interesting. It's not as quick and the engine is more boring (revs) but it's ~30k$ new and the same weight and power in coupe format. So a slightly more daily version for <60% of the price.
What can you get that trounces it for the price? Even a Golf GTI doesn't do much better (and you can't even get it in manual anymore).