These two seemed fairly equal to one another in strength and swordplay, and made up for eachothers physical differences. In fact, if I remember correctly, Saitou is one centimeter taller than Aoshi, and Aoshi is one kilogram heavier than him.
These are the characters post Kyoto Arc, so Aoshi has already found his new conviction in life and become stronger. Fight takes place where Kenshin and Shishio fought.
Who do you think would win?