Rumor has it that one of the plans for Season 3 that Proto Man was going to have a full-fledged Heel–Face Turn (rather than the temporary one he had in Season 2), with Wily building Bass and Treble as replacements.
Having Snake Man in the Mega X episode makes sense because most Mavericks are animal-based, as is Snake Man.
Time and time again over the course of the series, Proto Man is seen openly disobeying orders and even sabotaging Dr. Wily because of his personal vendetta against Mega Man. Since Dr. Wily is Proto's creator, it would have made sense for him to simply reprogram Proto Man and make him more obedient, and yet he never did. That's because he would have to accept that Dr. Light was right when he warned Wily that the guidance system of their prototype was faulty. Dr. Wily doesn't want to face that bitter fact, and prefers to deal with Proto Man's disobedience.
In "Brain Bots", Wily places Mega Man in a Death Trap. The trap consists of a Descending Ceiling with spikes. Unlike some death traps, Mega was bound to the floor as it descended. What pushes this into Fridge Horror is what Wily said about it; he uses it to recycle robots he no longer needs into scrap metal. Meaning he's done this to HIS OWN ROBOTS. What makes it worse is that some robots, like Fire Man and Star Man, were only in one episode and never seen or mentioned again...
"The Strange Island of Dr. Wily": Woodman was among Wily's group, until sustaining heavy damage towards the end. He isn't seen escaping with them.
In "Future Shock", Roll doesn't believe Mega is real at first, saying it's another trick of Dr. Wily's. Meaning Wily may have staged rebellions and incited false hope with a fake Mega Man.
In "Bro Bots", Wily's plan turned out to be replacing the city's leaders with robot doubles who would obey his every whim. Standard evil villain stuff, until you realize that Mega Man found out about the plan by finding a robot copy of Dr. Light. And given that he'd imprisoned the governor and Light over a pit of acid, Wily may have been going for a Kill and Replace scenario...
As noted in this review, Mega Man X pushed Vile and Spark Mandrill through a time portal that Sigma opened up to receive the MacGuffin for the episode. Meaning X is going to be deep in enemy territory when he exits the portal.
In that same episode, some have raised qualms about X's characterization and the lack of Zero. Things seem to be personal between X and Vile, with the former not caring what condition he's brought back in. And then you remember in X1, Zero died at Vile's hands.
In "Electric Nightmare", the cosmetic robot tried to use her razor on Roll, but she ducked. Looking at where the attack lines are and where Roll was in the preceding frame, she was trying to slice Roll in half.
In "Bad Day At Peril Park", Mega Man can't beat Hard Man in a straight battle, but when fires a blaster shot into Hard Man's mouth, this causes Hard Man to go out of control and explode — rather than just falling apart at the seams like other robots have, he violently explodes into bits of shredded shrapnel. Hard Man never reappears after this episode. Mega Man must have destroyed him utterly on screen. Holy crap.
confirms it was just a rumor.