I tried to write an 6502 program in C via CC65 compiler for the Atari 800 XE, it performed horrible NPS wise.
But I agree with syzygy and Chris, if someone skilled would give it a real try, to backport for example PeSTO to 6502 with 64KB, it would outperform all the classics, if not simply by evaluation and selective search being tuned.
We definitely do have better software now, more advanced eval, more advanced selective search, but it would be a challenge to backport all that onto limited hardware.
The hardware<->software progress is intertwined, co-evolution, you can not separate the one from the other.
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Srdja