Game Informer recently interviewed Splatoon Producer Hisashi Nogami & Co-Director Tsubasa Sakaguchi about Splatoon. They discussed developing the game as well as creating a new IP for Nintendo. GI asked if Splatoon had ever been considered to be created with established characters and the response was:
“With us, first we’re making the game, and then we think what kind of characters we would use with it, and obviously, one of those choices is established IP.
Of course, the most important thing is what matches. What matches with the gameplay and the abilities you are giving to the player, the play style, and ultimately what graphically will match the game you want to make. In the case of this game, we found that it really had to be new characters to would fit this game we were making. It would be kind of weird if Mario got splattered with ink and then exploded.”
So in the planning stages, Nintendo had thought about using characters they had already created, but decided none of them would work well with Splatoon and thus decided to go in a new direction with the squid/human idea.
Source: Gamnesia & Game Informer