While this hasn't particularly been fully explained,but there could perhaps be a hint that Protoboy was repaired by someone who found him destroyed after the battle between him and Robotboy. After being repaired the founder might have offered him to work for him/her and will always repair him every time he's hurt or destroyed thus can do his revenge.

Professor Moshimo have created Robotboy for use as a machine for defending and to communicate with humans as well. But having these three kinds of forms makes it easier to recognize what Robotboy and other of Moshimo's creations are depending the situation. For examples:

Deactivated: Robotboy is not activated when we see his head being shaped like a circle. The one thing Tommy use Robotboy as deactivated is like a toy when his parents are around him.

Activated: Robotboy firstly receives his ears by growing out and then can be used for both communication and defending. The way of Robotboy being activated can be used for battling and defend yourself from danger.

Super-activated: The most superior form only to use if the villain he battles with become's more berserk. The weapons becomes more advanced and powerful and can possibly overcome the battle.