You sure about that?
The Brown Yoshi appeared in 2 games before it was replaced by the orange Yoshi in Yoshi's Island DS. Afterwards, brown Yoshies have appeared in Yoshi Touch 'N Go as unlockable characters after some time in marathon mode, and also in the original Paper Mario as well.
So Brown does in fact exist, but why was it replaced and left as a minor? Only Nintendo knows the answer to that.