Acclaimed Flop: Despite positive reviews from critics and fans, the comics weren't the big seller Archie expected as with Sonic.
Ascended Fanon: Many fans theorized that there was a real Mr. X that Dr. Wily was just impersonating, which this continuity goes with.
Executive Meddling: Ian Flynn has claimed that Capcom was remarkably hands-off with the series, compared to the mandates he received from Sega—it certainly didn't hurt that the comic is overall a very close adaptation. However, one thing they put the kibosh on was making use of Hornet Man's unused female design, which was what led to the creation of Vesper Woman (who looks like it but isn't quite the same).
Fandom Nod: Possibly a coincidence, but the idea of Wily hiding malware in his robots' weapon data had previously appeared in at least one of the innumerable sprite comics that were everywhere in the early 2000s.
When Dr. Light is consoling Mega Man, he references The Megas, specifically "Message from Dr. Light", reciting a good portion of the song almost word-for-word.
According to an interview with Ian Flynn, the reason that Bubble Man went down so quickly, and to a weapon he's immune to in-game at that, was in acknowledgement of the fact that he's regarded as a complete joke by much of the fandom.
Air Man claims he cannot be beaten, likely a reference to the song "Airman ga Taosenai".
Proto Man faces off against a biker on a green bike in one issue, even calling him a "Green Biker Dude". This is, of course, a reference to the Ensemble Dark Horse Reploid from Mega Man X2's opening stage.
Another Archie Sonic connection, Ian Flynn was the head writer of both this and Archie Sonic.
Inker Kent Archer may be known to you as the former inker of Dr. McNinja.
Keep Circulating the Tapes: Like fellow comic Archie Sonic, the comic ceased publication and was taken off digital storefronts in 2017, though unlike Sega, Capcom didn't make any announcement. Trade paperbacks are incredibly hard to find, and while Boom! Studios have published a singleMega Man comic since, there's no word of reprinting the Archie run.
Quietly Cancelled: Already struggling in sales, the series ended at its 55th issue and "went into hiatus" according to Archie. But the last issue was pretty much a swan song for the comic doing a brief overview of events of future struggles that they couldn't cover and of later series of the franchise (X, Zero, ZX, Legends, etc) as well as the Short Circuit gag at the end essentially thanking the reader for their support. The cancellation of Sonic, combined with Udon and Boom Studios gaining the rights to make Mega Man comics respectively all but ensured that the comic can never come back.
What Could Have Been: One could have imagined how the comic would have handled the later incarnations of Mega Man have if it never got cancelled.
Ian Flynn also expressed interest in “Getting Volnutt off the moon” implying that had if the comic ever reaches the Mega Man Legends era, there is a chance for Legends 2’s cliffhanger to be resolved in the comics.
Per word of a Bumblekast episode, the original plans for the Gameboy games and Wily Tower was going to slot in before they got to the adaptation of 4, then things were changed over time.
Ian Flynn mentioned at least having an idea if he could've gotten away with using Bond Man for a story. It would've been a Free Comic Book Day issue with Rock, essentially, having a fever dream from a broken coolant system that would've been the Soccer adaptation, with Bond Man being the star player of the enemy team.
Other trivia
In continuing with the musical theme naming from the games, Quake Woman's given name is Tempo.
that they were correct, and hinted that, with the exception of Quint, who is treated as Rockman Shadow, they'd have to use stand-ins when they covered that particular arc.