Have Yoshi survive and succeed in starting a civil war, which ends with a faction winning and holding complete control over the city. In order to maintain power and prevent another war, they keep a powerful military force, which is what they will use to defend against the Class and eventually invande and settle the surface. The revitalized people of Lux replace the stagnant people of the surface (who will probably upload themselves into a virtual world or something as a response) and civilization resumes its evolution. From watching this show twice, this is what I gather Yoshi's ultimate plan was, given that he knew the conditions of the surface people, the Class and Lux.
As the ending of the show stands, the robot-tree-people might or might not evolve into full cyborgs and eventually go to the surface. The blue-haired guy was crazy and seemed to have only intended to destroy everything, but then why make the robots and his own feet grow roots when the fighting was over? Maybe he really wanted throw the fate of humanity wholly to evolution, whatever evolution might look like for robots with human heads and roots.