These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Base Breaker: Basilisx; people were split between those who believe that he was right in calling Mario, who has had a whole history of games fighting Koopas and other enemies, out on what might be questionable actions and morality, and those who believe that Basilisx is a hypocrite with a huge case of Moral Myopia, when also considering that Bowser and the Koopas have had a long nasty history of being repeated aggressors against the Mushroom Kingdom and their treatment of other races and Mario was being the defender in trying to stop their aggressive takeover.
Complete Monster: Mecha Sonic. As soon as he came into being (via Metal Sonic absorbing past models into himself), he destroys the Death Egg and forces it to crash-land on Mobius, causing an apocalypse. He then, while hunting down the Chaos Emeralds, also took the opportunity to kill Sonic's friends in extremely brutal ways (Tails by strangling him, Amy by beating her up, Knuckles by beating him up and then filling him up with machine-gun processed lead, and Cream and Cheese by apparently blowing her head off), and had wiped out most, if not all, of the planet's population and turned almost half of it into a burning wasteland. He was also the reason for Shadow's current personality, because he killed Rouge and Omega, the only people he could call his friends. As soon as he arrived at the Mushroom Kingdom to recover the Chaos Emeralds, he also killed a Goomba who found a Chaos Emerald simply because he didn't give it to him, even though there was absolutely no way he could have known that was a Chaos Emerald. He then mercilessly beats up Yoshi to gain his chaos emerald (and says that he would have killed Yoshi anyways even if he did comply to his request). He later brutally killed both the Koopa Bros and the Axem Rangers X and destroyed Yoshi's Island. Not just scouring the surface, but hitting the island with a Sphere of Destruction so violent that it vaporized the entire island.
To wit: You know how Mario uses the Fire Flower often in this series? The most he does with this power is throw fireballs or fight particularly ferociously. The crowning moment in this is Sonic showing exactly what someone can do with the Fire Flower's full potential with the use of speed and Chaos Control — demonstrating, in order, a series of incredibly-intense rapid-fire balls of nitro-hurt, decimating enemies Sonic Unleashed style, and creating a time-delayed vortex of flames. All of this in under a minute.
In Real Life, getting Newgrounds to update the site just so he could put up Episode 8.
Luigi using the powers of his Tanuki suit to reverse Basilisx's petrification attack, then hitting the mad Koopa with a sneak attack to save Mario.
How about the fact that the author, despite his confession to no longer being able to work on the series, persevered long enough to make the animation of Luigi saving Mario from Basilix available to the public?
Back To Mad, during the intense brawl on Yoshi's Island before Mecha Sonic showed up.
At least two of those have some sort of meta-CMOA to them as well, The Doomsday Zone remix was originally part of an OC Remix project that played on the "old-timey radio" feel of the opening, only to rock the 'eff out. "Back To Mad" was made famous for being used in a flash animation called "Rockman Neo", which depicted a dark third generation for the Mega Man franchise (before Mega Man ZX happened, that is; Neo, incidentally, is what the Mega Man Legends series is known as in Japan).
How can we forget Crisis City, used when Sonic becomes Fire/Solar Sonic in episode 8?
Evil Is Cool: Mecha Sonic, as mentioned above, gets a following being the most Badass character in the series, having taken down characters with Chaos Emeralds without using any himself, and pulling off a Curb-Stomp Battle on Mario and Sonic at the same time without any Chaos Emeralds.
Luigi's fighting style is this as well. He's the only one among the main team that's been relegated to the traditional Player 2 position in the past, rather than Player 1. He's by far the best team player among the group, and his most badass moments are when he comes flying in to back one of the others up.
Growing the Beard: Arguably around Episode 3. At this point the stakes have been established and the writing and pacing have hit their stride. As for the animation and action sequences? The action before was decent but slightly stilted, repetitive and drawn-out. It's around this point that the action fully grew into the slick, inventive and spectacular action that defined the series that would only increase in ambition as the series went on.
Holy Shit Quotient: The ratio approaches one during a few of the fight sequences. For some, it actually exceeds 1.
Jerkass Woobie: It is heavily implied that the reason for Shadow's current Jerk Ass nature is due to rage in regards to Mecha Sonic murdering Rouge and Omega, the only two people he could ever openly consider friends.
Just Here for Godzilla: The fight scenes are undeniably magnificent, so it's no surprise that some viewers don't really care for the plot or jokes.
Mis-blamed: Contrary to popular belief, Shadow the Hedgehog did not hit Mario during the fight with the Koopa Bros. in Episode 4. He was actually knocked into Mario by Black Ninjakoopa offscreen.
Moral Event Horizon: Mecha Sonic destroying Mobius along with its inhabitants, including Sonic's friends. And this is only the backstory. He gets worse from there.
IN FACT LET'S COMPILE A LIST OF HIS ATROCITIES TO PROVE JUST HOW WORSE HE GETS.
The aforementioned murder of Sonic's friends, all in brutal fashion.
Kills a random Goomba just for being understandably confused and therefore not reacting quickly enough for his liking.
Destroys Yoshi's Island (after brutally slaughtering the Axem Rangers X), killing the Koopa Bros. and numerous members of the wildlife in the process AND leaving every Yoshi homeless.
Strawman Has a Point: Shadow proposing to collect the rest of the Emeralds and stop Metal Sonic over saving Peach is recieved with disgust. Neverminding the fact that Metal Sonic already ruined a planet and Bowser never harms Peach.
Tear Jerker: Two scenes — Sonic's flashback in Episode 4, and the argument early on in Episode 8. In the latter, the music really helps.
Sonic and Shadow's bickering in episode 8 should be considered Narm/Narm Charm if you'd been paying attention to Mario and Luigi's reactions.
Alvin-Earthworm's announcement that he is ending the series, simply titled, "I'm Sorry..." You can just see the disappointment in his words.
I have drafted this journal several times before but never had the courage to actually post it, but now I think it's high time I did this.
This is a very difficult thing for me. I have had this on my mind for quite some time now and I have no doubt that it will be a very unpopular decision, but I think it's time I finally lay Super Mario Bros Z to rest. I have been fooling myself into thinking I would continue the series because part of me really wanted to see it finished. But the fact is, it is a time consuming process and I have grown tired of working on it. Sprite animation no longer has the same appeal to me as it did several years ago. What was once a fun hobby of mine has now turned into a chore from the constant demand, which clearly shows from the lack of updates since episode 8 was released. I could blame my lack of motivation on my monotonous job and the impatient fans. (Not saying all my fans are impatient, of course. I'm only referring to the Vocal Minority). I have been keeping the series on life-support this long, hoping that some day my creative spark would return to me. Unfortunately it never did.
In any case, I would like to thank everyone who stuck by the series this long. It really pains me to do this to all of you after years of false promises, but it's high time I gave myself a reality check.