No killing Skeletor, that is not the way MOTU works. This isn't like other franchises because the villain is more iconic and interesting than the hero. There are many MOTU fans that consider Skeletor to be their favorite character. Not just favorite villain but favorite overall character. There are many fans that root for Skeletor and like him better than He-Man. Killing Skeletor would be a slap to the face to a large portion of the fan base. Skeletor always gets away as to show evil can never truly be defeated. Skeletor and He-Man are like the Yin-Yang. The Yin can never actually defeat the Yang. One side just exists to balance out the other.

He-Man vs Skeletor is a true duality. Their relationship is like summer and winter, night and day, sun and the moon, life and death. It is a balanced cycle like the ebb and flow of the tides. This the natural way of things.