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If we are talking about the early naughts (since your S2000 is from that era), Honda vs. BMW is no comparison.
That era was Honda's high water mark for reliability; the only real issue was their automatic transmissions tended to implode, but I avoided that issue by selecting Honda's excellent 6MT on my '04 TSX (which I drove for a decade with exactly one out-of-pocket repair; the cruise control switch of all things). BMW's of that vintage suffered endless issues with the cooling system combined with the infamous E46 rear subframe issues, countless electrical gremlins, suspension issues, etc.
That said, we are now entering an era of DI turbo engines, and BMW had a head start on virtually everyone in this area. Honestly, I'd probably trust the N55 or N20 much more than Honda's new 1.5 and 2L turbo engines, considering the disaster that was Honda's last foray into forced induction (the original RDX). Honda probably is still more reliable for non-engine components, FWIW.
Personally, I wouldn't own any German make out of warranty, except maybe a naturally-aspirated Porsche. The entire appeal of driving a Toyota or Honda is that you know it'll be reliable well into 6 figure mileage, it'll just bore you to tears in the meantime (S2000, NSX, and GT86 excepted).
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