The plot of MGS1 is that the genome soldiers are all enhanced by the introduction of Big Boss' DNA because Big Boss was just that good at soldiering however in MGS3 Big Boss gives an extended monologue where he's extremely autistic about guns so I personally believe the genome project just makes you autistic send tweet
The genome soldiers are inferior because they merely adopted the autism, however Snake as a direct clone of Big Boss was born in it, molded by it,
i mean that goes in line with them giving snake the “inferior” genes and him still being better than them. they thought big bosses autism was a weakness when it was his greatest strength