Shishio would lose. His primary strengths are not so much skill, but phenomenal strength and battle endurance. These
traits would not constitue as much a threat towards Enishi, who has displayed near-equal strength and a ridiculously
high pain threshold - he absorbed kenshin's Kuzu Ryu Sen technique, then was smashed to the ground from 3 to 5 stories
up, but remained completely unfazed, stating it did not hurt at all. This resistance to pain would also make Shishio's
Homura Dama useless, since the fire is more for inflicting distraction than injury. Enishi is also extremely fast,
capable of not only blocking all 9 Kuzu Ryu Sen (2nd fastest technique in series) slashes, but moving quickly enough to
strike Kenshin before the first slash is even completed.
Enishi is also the only character in the entire series to be shown consistently dominating Kenshin in a battle. Shishio
was surprised several times and was struck in many vital points, including 3 blows to his head, which would have been
fatal had Kenshin used a real sword. Enishi in contrast faced Kenshin when both were going all out, but was not even
touched by Kenshin's sword until being struck down by the Amakakeru Ryu no Hirameki, and in fact inflicted numerous
serious injuries upon Kenshin.
Finally there is Enishi's Kyokeimyaku (Nerves of Insanity), that enhance his speed, strength and reflexes to superhuman
levels. In this state he is the de facto strongest swordsman in the entire series, capable of matching, if not
surpassing, the Tenken Seta Sojiro in speed. Had Kenshin not possessed a (rather useless) technqiue (that Shishio lacks)
to disable his equilibrium, Enishi would have had an assured victory.
Shishio has absolutley no edge over Enishi. There is no way he could win.