In an Sega.jp Meisaku interview with game's creator Kotaru Hayashida (aka Ossale Kohta), he was asked why did he wanted to use jan-ken-pon (rock–paper–scissors) in boss fights. And he responded:

"That was also one of our concepts to differentiate our game from Mario. It a very fanciful, absurd idea. There were various reactions, like “What the hell! Isn’t this supposed to be an action game?!” or “I lost the rock-paper-scissors match and its Game over!? This sucks.” Definitely, for people who are good at action games to lose everything and Game Over because of a rock paper scissors match… yeah, that sucks.

The staff at Sega shared these concerns, but I wanted to know how players would react to it, so I left it in."