Perhaps part of the reason they chose to abandon him was the anomaly of his presence. In an alternate universe where Mario was disgraced for failing Isle Delfino and in turn the world, he would have faded from the public eye. Besides, in this timeline, Splatoon would take place eons after the Delfino mess. It's not hard to imagine the world of the Inklings as a broken piece of the Mario timeline, a shifted piece of a parallel universe in which our heroic plumber failed.