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.
Arc Fatigue: The final battle of Part 1, which takes over ten chapters before it finally comes to an end, could noticeably have been cut down by a couple more if some Padding was cut and some chapter's events merged together. Averted in Part 2's final battle though.
Big Lipped Alligator Moment: When the heroes are taking the Stargadd to the Origin Temple in Part 1, they are flung through multiple dimensions, where they see, as quoted from the text: "massively grotesque worms swallowing entire galaxies in one bite, titans made out of cosmic radiation juggling suns in the palm of their hands, and a massive spider walking along a web made out of approximately one million planets". Naturally, none of this is brought up by any of them once they arrive at their destination.
However, when this happens again in the Extra Chapter, the bizarreness of it all is noticed and Lampshaded by Alex as he witnesses it all:
Moral Event Horizon: Joe Dark's Vicious slaughtering of the Genesis Samurais definitely qualifies under this, more so considering how he basically spits on their honor after their deaths. This trope is even discussed afterwards by Alpha who even says straight out that "You've crossed the horizon, now we're gonna make you fall."
Cackletta Sacrificing one million lives and destroying Rogueport as the Shadow Queen just so she can prolong her own life is merely ONE of many instances where she crossed the line.
There is also Dimentio, who crossed this when it is revealed that he purposely ruined Blumiere and Lady Timpani's life just to further his plans to get the Chaos Heart. What is particularly bad about this example is that this is a MEH crossed by hundreds upon hundreds of alternate universe Luigis as well.
The "Higher-ups" cross this big time in the What-If for Part 1, where they wipe out Plit and turn Mario (The New Elemental Overlord) into their personal, mindless slave in that timeline. The worst part about it is when they completely ignore Eldstar's plea and state that everyone in the universe is expendable.
Nausea Fuel: Going by the description in the narrative, It really isn't a good idea to think about where Sin Aqua's hoses are inserted to... Also counts as Fan Disservice.
Iron Woobie: Gemini. As revealed in his Origin chapter, he was once a normal Koopa living in Koopa Village, he was taken away one day by Bowyer and brought to Smithy's factory, where he was swiftly forced to endure a heart transplant while awake, and quickly mutates into a demonic creature. Even after breaking free he is ostracized by his people, and leaves his hometown on his own accord, along with his friend Kooper and potential lover Kaylie. He then travels alone through the desert, enduring the pain of sand against his flesh until Alpha picked him up and the rest became history... And in spite of all that he still goes on day after day without grieving over his losses. Though he eventually just becomes a plain old Woobie after breaking his iron will to lash out against Smithy in Part 2
Stoic Woobie and Jerkass Woobie: Alpha Big time. It is greatly implied through his memories that he has endured through a LOT of crap in his life, the most prominent being the violent loss of his father/mentor Commander Zeta, which drove him to get revenge against Cackletta. There are times where his stoic demeanor starts to crack, but otherwise he keeps the facade up around others, even up to Cackletta's demise