The F20C has decent efficiency actually, lowest BSFC is 242g/kWh which is really quite good when you consider that a newer 2GR-FSE with greater per cylinder displacement and direct injection has a peak "below 230g/kWh" (according to Toyota). I wouldn't read too much into stroke and stuff, on production engines that's not going to be the thing that decides fuel economy at all.
The problem is the transmission gear ratios, if you're comparing it to a Mustang. The Mustang has a "suggested" 1-4 skip shift in the manual transmission which really helps on the EPA cycle. The S2000 has very bad gears for fuel economy, its 60mph cruise speed is well into the 3000s. Despite all that, you'll probably notice that Mustang 5.0 owners are typically getting lower fuel economy than S2000 owners.
In general sports cars with fast acceleration suffer on the EPA test by default because the EPA test has standardized acceleration/deceleration, which requires them to run their engines at very low outputs (see Lotus Elise). Manual transmissions usually get shafted because the EPA test has a predetermined shift schedule that is bad for fuel economy compared to the typical automatic shift logic, and because manufacturers assume manual transmission buyers want a "sporty" experience and shorten all the gears.
TLDR: don't trust the EPA ratings too much, and back in the day when no one gave a crap about fuel economy they didn't have proper cruising gears in the transmission.
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