- Awesome Ego: Commander Sev at the world summit. He's constantly spouting propaganda and has the biggest ego out of anyone in the summit, but he's just so hilarious it's hard not to love him for it.
- Anvilicious: The story beats the idea "there's nothing wrong with Poképhilia" constantly, and introduces numerous Straw Characters that oppose it that serve as sounding boards to argue such against. Other stories such as A New Ranger have toned it down a bit by emphasising that there were genuinely abusive relationships on Earth in addition to those who were unfairly persecuted.
- Broken Base: Zeus' readers have been divided ever since the conclusion of Book 1, with many drawing some very uncomfortable comparisons to The Conversion Bureau; only in reverse. There have even been some debates regarding Arceus' behavior, citing him as not only inconsiderate, arrogant and impulsive to a fault, but misanthropic to such a degree that he can't even bring himself to trust someone unless it's a Pokemon. There are others however, that see him as a Well-Intentioned Extremist who simply had no choice in the matter.
- There are also many who are calling out Zeus of being passively misanthropic as well, with his counterarguments to defend humanity being weak, while still painting them in a negative light. Not at all helped by readers who have gone on to see Poképhilia as a weak Plot Device that doubles as a Romantic Plot Tumor, to distract the characters (and the reader) from the more pressing matter of how the majority of the human/Pokemon might really be coping with their predicament, and how Arceus has essentially committed genocide.
- Creator's Pet: Belle, who is constantly threatening mindrape on people she disagrees with and getting away with it every single time. The one time she goes through with it was treated as heroic for not going all the way. The author only punished her due to fan-pressure, and even then he tried to make her look like the victim in the scenario.
- Designated Hero:
- Cresselia, the legendary who came up with the "Brilliant" migration plan. While Arceus may have been the one to carry it out, he was called out several times, admitted to the plan having been too hasty, and later began to take steps to atone for it. Cresselia on the other hand has done jack shit and remains a Karma Houdini.
- Mewtwo has shades of this as well, due to an apparent lack of ethics when it comes to his psychic powers. It first comes up when he somehow intimidates a member of Celestia's council into shutting up - admittedly, said stallion was being a bigoted snob regarding Pokémon sapience - but he follows it up with his brutal Mind Rape of Luke, which left the latter a completely broken mon, with no stated excuse at the time beyond his curiosity about Luke's unusually powerful mind for a Gallade. And while he claims to regret doing this, a subsequent appearance (written by a different author to the above scene, it should be noted) showed him misrepresenting his actions as believing he was investigating a possible threat to the palace, directly contradicting his own POV from A New Way Chapter 53 - as a result, he now appears to have lied his way out of trouble, including the initial house arrest pending possible criminal charges that Arceus had previously agreed to, while even keeping his ambassadorial position at Canterlot Castle. In addition, his description of an offscreen confrontation with Luke's teammate Kasai, which left the Arcanine believing he had fleas for ten minutes, suggests that he has learned absolutely nothing about psychic ethics, from his or anyone else's recent experiences.
- Harsher in Hindsight: Belle's threats to lobotomize any threats toward her relationship with Gene... Let's just say Hastings got a first-hand experience, to a point that at least a couple of readers feel it would have been more merciful to kill him.
- Said first-hand experience even left Hastings on suicide watch, which ended up paying off as of the closing chapters of Book 1.
- Seasonal Rot: The fic slowly but surely began to lose its way as it progressed. The addition of more and more sub-fics resulted in constant filler to introduce the other author's characters, who at times seemed hellbent to out-Mary Sue each other, and whenever one author stalled, the verse ground to a halt. The long gaps between chapters also resulted in many continuity errors, with the prologues being contradicted several times. The fics getting preachier in general didn't help. As of writing, two Pokemon generations have passed and the "Friendship is Magic" cartoon has ended, making any attempt at a return both unlikely and an uphill battle.
- Strawman Has a Point: Prince Blueblood, with his xenophobia toward Pokemon. While he's against them out of his sense of superiority... Arceus moved the entire Pokemon population to Equestria, one of the first he encountered was a tempermental hellhound, one nearly killed Discord simply because of differing ideology, and they torment him for his prejudice rather than try to convince him to get to know them. In the story's context, he's still a Jerkass, but it's not without merit. The problem stems from him viewing all Pokemon in a bad light because of the repeated impressions he gets from the Pokemon he encounters.
- Wangst: Luke can come across as this, as most of his appearances in the main story consist of little but whining about his life. Less so in his own story A New Ranger or A New Mind, where he's much more of a Stoic Woobie up until the Mind Rape from Mewtwo that resulted in the above.
- They Wasted a Perfectly Good Plot: Cofagrigus. Given much of the fic focuses on the opinions of former humans who had been turned into pokemon following the migration, it would have been interesting to hear the opinion of a human who had been transformed before the migration. Instead, we get a trite Monster of the Week. Later, when Shauntal debuts, the opportunity presents itself again, and is again missed.
- What an Idiot!: Its revealed that Paranoia has been arrested multiple times for his racist behavior, yet he still doesn't learn his lesson.
- You could count all the more fanatical members of Hastings group. Koga starts by deducing that it's perfectly reasonable to attack Equestrian law enforcers, Surge just up and charges straight into Ponyville to somehow arrest a single fugitive by force and later Brandon deciding it's a good idea to attack Latias, despite being her being the personal family of Arceus.
- The Woobie: A lot of the trainers, either due to their experiences on Earth (many of them having suffered at the hands of human criminals or prejudiced law-enforcers) or due to their struggle to adjust to their new bodies. Gene, and Jayce stand out in the former category, Korrina and Misty in the latter, and Abby and Vincent in both. A number of Pokemon, especially those in A New Ranger and A New Mind, have also had horrifying experiences on Earth.
- Jerkass Woobie: Korrina falls into this territory due to her treatment of Gene and Belle, though she gets past it eventually.
YMMV / A New World, A New Way