After Tails gets blasted in the face by a Ballade Cracker, he says he's had worse and pulls through okay. Remember how Tails can take loads of punishment (and always comes back from death) in Sonic the Hedgehog 2 and Sonic 3 & Knuckles when he's Sonic's partner?
There is another layer of brilliance when remembering that Sonic 3 & Knuckles were originally sold as 2 parts to 1 whole story. Tails specifically mentions the Launch Base Zone; the last level of Sonic 3. When played separately, Tails does not show up in the "& Knuckles" portion of the story except for his Big Damn Heroes moment at the very end. If all the events of the games are Canon to their world, this implies Tails was injured and sat out the 2nd half of the story.
The way Eggman describes the process of plugging a Devil Core into Chaos 0 in order to create the Chaos Devil does this on the entire Devil Series of robots from the classic series. The Devil Core is the weak point because it's the only working component. Everything else is a substance being manipulated by the core.
Eggman works on the Wily Egg's battle stations and main design while Wily works on its fortress defences. Eggman's Death Egg is much more heavily armed (and larger), but Wily's castles have more inner defences in the form of multiple fortress levels with bosses at the end of each.
Two of the Genesis Unit react pretty strongly when Mega Man attacks with the Tail Wind weapon, even ignoring their current opponents. This may make little sense, but Hyper Storm H. was never the brightest of the three in the first place, and Buster Rod G. is significantly weak to the Air Shooter, another wind-based weapon, both times he's fought.
Why are the Death Egg Robot and Wily Machine 9 the basis of Egg-Wily Machine X? Because one thing they share in common is having alarm sounds in their boss themes!
At the end of the crossover and Mega Man's first issue following, no one remembers what happened. How could that be? Eggman interfering with Sonic's Chaos Control. The Super Genesis Wave had already altered reality and Eggman's attack on Sonic's Chaos Control massively altered Mobius and the multiverse. As Archie considers Mega Man's universe an alternate universe connected to Sonic, it, too, was affected by the snap back. That explains why Mega Man is utterly confused about how everything was when he and Break Man return.
Why does Wily react so strongly to Eggman attempting to kill Light? Well, aside from the fact that his entire motivation is to prove he's better than Light (which can't be done if Light is dead), maybe Wily still has a bit of respect for his old friend and colleague.
When presented with the blue chaos emerald, Dr. Wily exclaims "Sweet mother of Edison!" Now consider that Edison's first name was Thomas, the same as Dr. Light, and that Dr. Light's appearance is based partially on Thomas Edison.
Well, obviously Thomas Edison existed in Mega Man's world at one point. It's still on earth it just in the year 20XX.
Why is the silver chaos emerald in a bank vault in Mega City, a completely different universe from where it was previously? Because otherwise the doctors would have had no way to casually draw Mega Man into a fight with Sonic!
The Genesis Wave reset both universes and the locations of all the Chaos Emeralds. When both universes were recreated, the Chaos Emeralds were scattered between them. The silver emerald appeared in Mega City's bank vault.
Why do Super Sonic and Super Mega Man need to resort to their No Kill like OverkillOne-Hit Kill? Well, the Egg-Wily Machine X has already shown that it has a Healing Factor when it restored all the damage done by Proto Man and Knuckles. Even though the two were doing plenty of superficial damage, with the machine's ability to regenerate in place, the only thing that could put it down for good was a blast of such magnitude that there would be nothing left to regenerate.
There are several spots where, if the doctors had managed to check their egos or paranoia, they could have easily won.
Second-most telling is the part where they curb stomp the heroes after they are weakened from their duel with their evil knockoffs, and then very deliberately don't finish them off so they can indulge in some Evil Gloating.
Most telling is that the doctors got Sonic and Mega Man involved at all. They wouldn't have known about each other and joined up if the doctors didn't attack them and set up Sonic and Mega Man's initial battle to begin with.
There's also the fact that Sonic got the idea to use the Chaos Emeralds after hearing Dr. Light say the word "super." Dr. Light only said that because he had no E-Tanks to give Mega Man and suggested he use Rush's Super Adaptor, meaning Roll didn't have any on hand to give to the Light Robot Masters who would in turn give them to Dr. Light. If Dr. Light had kept up on his supplies, the Doctors would've won.
The doctors abduct nine of Sonic's friends to make into Roboticized Masters. Sonic only witnesses the abduction of one. With Copy Robot's Teleport Gun and the team of Bass and Metal Sonic, they could have easily grabbed more if they had wanted. Heck, they could have probably grabbed Sonic himself if they weren't so dead set on messing with his head. In fact, Sonic himself does get roboticized in the sequel comic.
Devil Cores. If they can turn Chaos 0 into the Chaos Devil, what could they do to any other liquid life-form?
Worse, could Wily turn any body of water into a Devil? Imagine him forming a Devil Army from an entire lake!
Snively had a cameo in the crossover, but was never seen escaping the Wily Egg. The next arc in Sonic Universe, Pirate Plunder Panic, doesn't show him. It does show the ship being commandeered by a rogue version of Metal Sonic and ultimately shot down by Burning Blaze. Snively might be dead now.
