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Who wins?

Assuming their weapons could actually harm them, He-Man would effortlessly solo. He has a level of physical superiority far above any character in Samurai Jack IIRC.

He-Man being there renders Lion-O more or less useless. He-Mans plot device magic sword would probably work just fine, and he has insane levels of strength and speed.

As KMC's only Thundercats historian, Lion-O could potentially solo as well. While he hasn't shown the plot-strength He-Man has, he has:

-easily cut through massive boulders
-bested Panthro who likely a 100+ tonner in the Trial of Strength (one of the test to become Lord of the Thundercats)
-lifted and flipped over the ThunderTank as easily as pressing X in Halo to flip the M808B Scorpion
-dodged and deflected multiple incoming lasers with ease.

Don't forget about pulling Safari Joe's ship back down to Third Earth as it was attempting to escape the atmosphere. (Still nowhere near as impressive as He-Man holding back Horde Prime's starship with warp engines running, but it's nothing to sneeze at.)

I would be willing to bet the Sword of Omens would work better against Aku then the Power Sword would.