- Alternate Character Interpretation: Blues is a flat-out jerk at times. He has no problem manipulating Bass into attacking an injured Rock or threatening to shoot Kalinka Cossack. Even worse is the time he set Copy-Mega Man up to commit suicide.
- Angst Aversion: While a big selling point of the series is that it's a darker, more serious look at the Classic series, some fans shy away at just how dark it can get. Particular points are with Blues, who manipulates Bass into attacking Rock and threatens to kill Kalinka (with his plan hinging on people believing he would), Bass, who has no redeeming qualities and brutalizes Auto as a warning, Copy-Mega Man, who is tricked by Blues into killing himself after growing beyond his programming, the Stardroids, who kill almost the entire cast, Duo, who's a Knight Templar willing to kill anything in his way, and the entire Mega Man 9 storyline, which had Dr. Light argue against the expiration date for hours only for it to pass, Wily and Reggae visiting him in jail to blame him for not doing enough to stop it, and the MM1 Robot Masters getting defeated by the 9 set while Rock goes to fight because it's his duty.
- Big-Lipped Alligator Moment: The Soccer and most of the one-page strips compared to the main plot. Of course, it turns out that some of the comedic elements there, like Auto's tendency towards mad science and Duo's Knight Templar status are traits they have in the main story and effectively foreshadowing. When Duo shows up in Gigamix, it is definitely not played for laughs. The antics of the part-timers are also a subversion, as they act that way even in serious storylines.
- Growing the Beard: Gigamix features a more refined art style and plot, even more so than its predecessors. It also sees an entire arc of humor in Battle & Chase. And then Ariga rereleased it with improved art.
- Harsher in Hindsight:
- Duo in the Bonus Strips from Megamix is an absurdly strict, hypercritical, hair-triggered Knight Templar. This is played for laughs. Come the 'White Giant' in Gigamix Vol. 2. He's an absurdly strict, hypercritical, hair-triggered Knight Templar...who utterly decimates Wily's forces almost down to the last bot, and was willing to destroy all the Light Bots too just for being in the way. This is not played for laughs.
- The interviews found towards the backs of the Megamix Udon Double Subvert this with Mega Man Legends; it shines some light on why its infamous third installment was cancelled. When Ariga and Inafune are discussing the series, Inafune says that Legends was the Oddball in the Series, and was unique in that it was the only seriesnote that put Capcom "in the red". He says that Capcom did not recoup its development costs. In the end, it's played straight, as Inafune says that he hopes one day the time will come where he can revive it.
- Ho Yay: In addition to the Roll/Kalinka Les Yay, one of the short comics shows Toadman (a Cossackbot) hibernating with Snakeman (a Wilybot). In character profiles from one of the games, there were some implications that Snakeman was Toadman's Stalker with a Crush, so this may be another case of Shown Their Work. There's also a scene in Battle and Chase that may be a little more than just Sempai/Kohai: the other characters find the whole thing very awkward...
- Jerkass Woobie: Skull Man and Copy Mega Man.
- Les Yay: Kalinka and Roll. In the story where they battle Skull Man, they have to huddle together to avoid Kalinka freezing, with Roll nearly overheating herself in order to save her life.
- Moral Event Horizon:
- Blues seems to have gone over this when he threatens to shoot Kalinka Cossack. It turns out it's a Batman Gambit to prevent Rock from dying, and probably the Cossackbots caught in the crossfire too, and Shadowman assassinating Rock. It only worked because they thought he'd really do it. Everyone is saved, except for Copy Mega-Man.
- In Shadow Man's opinion, Blues' actions during The Greatest Enemy In History were far over the line. After Shadow Man, whose main trait until this point was loyalty to Dr. Wily's orders (he is a Ninja, after all), went against his orders to use the confusion of Roll telling both Mega-Men to stop fighting to rescue Copy Mega-Man and give him a fairly heartwarming talk about how he could become his own person with his own life, realizing that the whole thing was a Shoot the Shaggy Dog because Blues had set him up to commit suicide via Heroic Sacrifice was unforgivable.
YMMV / Mega Man Megamix