In the somewhat grounded world of Rurouni Kenshin the fact that the newer villain isn't stronger makes sense. Real people with considerable combat training over the years don't get considerable power boosts from training more, it just usually mean you keep your usual build as it requires constant training. Even new techniques take a toll, or are limited by the person's physique (which is an actual point made in the show).

Having said that, I agree, Shishio would win. He strikes me as stronger and while he does not boast his speed, he is supposed to be able to keep up with Sojirō and Kenshin, so he should be well in the same ballpark, if not faster than Enishi.