"In Japan, Boshi's name is Washi (i.e. "Bad Yoshi"), created by combining the word "Yoshi" with the Japanese word for bad, "Warui". As such, Boshi is to Yoshi as Wario is to Mario, or Waluigi is to Luigi."
Though he's never interacted with Wario in any game, I've always associated Boshi with Wario. Would love to see them appear together in a game one day. (would love to see Boshi return in any capacity, really)
I realize that Square owns the rights to all of the original characters in the game, but seeing as how Boshi is a Yoshi, and Nintendo owns Yoshi, they should be clear to use him, right?