The "Robotboy = Pinocchio" equation seems simple at first: Robotboy wants to be a human, just like Pinocchio. But remember how Pinocchio is/was a puppet? In a sense, Robotboy is a puppet, too — he does whatever Moshimo/Tommy/Gus etc, tells him to do because they're his friends, but Kamikazi can also control him in a different way.
It is rather odd that there is a "Protoboy = Proto Man" equation. But something Hilarious in Hindsight happened in "The Old Switcharobot": Protoboy (in Robotboy's body) attacked Moshimo because Protoboy believes Moshimo loves Robotboy (and Robotgirl) more than Protoboy. Years later, in the Archie Comics, it is revealed that Proto Man joined forces with Wily because he thought that Dr. Light replaced him (Proto Man) with Mega Man and Roll. Word of God is that, if there was a Series 3, Protoboy would have had a redemption arc, and I believe we'd have a scene between Protoboy and his girlfriend similar to the scene between Proto Man and Quake Woman in issue 35.
Both Robotboy and Robotgirl are basically walking weapons platforms with the minds of children. No wonder them falling into someone like Kamikazi’s hands is such a cause for concern…
We never find out what happened to Evil 17 at the end of "Double Tommy", and considering that he was in trouble with Kamikazi and Constantine for ignoring Kamikazi's orders to capture Robotboy, his fate probably is anything but nice.
Something noticeable about Protoboy. In the flashbacks shown in “Brother”, he’s shown to be more facially expressive then the Perpetual Frowner we know him as, screaming as he tries to wriggle out of the restraints Kamikazi placed on him in pre-reprogramming and laughing with a grin on his face as he blows up his lair. Meanwhile, in the present, he doesn’t really make any expression apart from a perpetual toothy grimace, an Oh, Crap! look at the end of "Brother" before he’s blown up, and when he's transferring to Robotboy's body in "The Old Switcharobot" (neither of which involve him moving his mouth). It could be that Protoboy was locked away for so long that some of his internal wiring was damaged from underuse. This is supported by how in other moments where he's expressed different emotions like shock or surprise, he always keeps the same face, and when he switched bodies with Robotboy, he was shown to be able to fully facially express himself, while Robotboy could not while in his body.
After Protoboy was deactivated by Constantine, it's shown that Kamikazi put him in a reject closet. In that state, Protoboy was harmless — why didn't Kamikazi just take him and reprogram him again to be less evil?
If Gus' parents are Amish, why are they living in the city?
Maybe they want their kid to live with all the other kids, despite their culture?
