The main purpose of inboard flaps (other than increasing the upper surface of the wing, thereby giving one greater lift at slower speeds) is to make sure the inboard part of the wing stalls first. When you add flaps to the wingtips (i.e. flaperons), then you are inducing added drag at the wingtips, thereby increasing the likelyhood that the tip of the wing will stall before the inboard section. This leads to a bad situation, at a very bad time. Tip stall is one of the quickest ways to crash an airplane on landing.
Remember, to stop flying one MUST stall the wing. By adding the flaps inboard, not only do you maintain full throw of the ailerons, but you also create drag which will slow the plane down, while creating more upper surface area, therefore giving you more lift at slower speeds, and (when the time is right), at an altitude of about 1 inch, you reach the stall speed, the inboard part of the wing stalls, and the plane sits straight down on the runway. Way better than the wing tip stalling, the wing dropping to one side, and the plane coming to a nice, four point cartwheel "stop."