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.
Broken Base - Alignments. Game of choice. There's a lot to argue over.
The Persona sub-series. Many of its fans are unaware of the main series, and some of the few that do bash the games for not being more like Persona, much to the ire of the main series fans. There are some people that even love the games but still hate them for their overshadowing popularity.
Draco in Leather Pants - There is nothing wrong with liking Chaos. Remember, though - that's the side that, while wanting to preserve Humanity, was the one to put the Z-ClassApocalypse How on the table or desires a Social Darwinstnote and by Social Darwinist we mean 'rule by the person most capable of killing everyone around them' world with no restraint whatsoever. Just saying.
It really depends on the game rather than those two being the only options. Chaos is portrayed far more positively in Devil Summoner 2 Lucifer and his manipulations aside and not every game wants a world of Social Darwinism. Not to mention the choice is between a Z-Class or endless cycle of X-ClassApocalypse How till all of humanity's free will is taken away by God.
If you were wondering what the above spoiler means, it refers to the fact that Lucifer tricks a young man, trying to save his sister from a Fate Worse Than Death, into kick-starting the apocalypse, while at the same time defacing the timeline. On the other hand, the original timeline's implied to be Shin Megami Tensei I, of all places...
Long story short, Lucifer's interest in Humanity has varied widely, and it's still the matter of intense debate. There's a reason half of everything he does belongs to the YMMV tab. Unwelcome meddler or radiant savior? And let's not even start with Law...
Probably doesn't help that Lucifer is turned into a good character in SMT 2, and siding with him arguable has the best ending, but his actions are a lot more questionable in the rest of the series
Fridge Horror: It's been explained that God is not the source of all evil in the series, and that something in the Universe is causing God to be Evil. Okay, um, what could be soevil that it makes God (y'know, the guy who made everything) evil?
Even worse. According to Christianity, God's very nature is love itself. What in the name of everything holy could possibly have corrupted love incarnate?
However, this could also be a reflection of exactly what's wrong with him creating Knight Templar Angels as well. As SMTII makes it clear that the Archangels own psychotic belief can give rise to a fake YHVH. If their own belief can create a fake one, then doesn't it stand to reason that angels in general can make God fit their view of their creator?
Ho Yay - Meet Persona. Meet Nocturne. If it's Mega Ten, there's porn of it. Usually in this variety.
My Real Daddy - Kazuma Kaneko and his artwork. The series just wouldn't have been the same without it. The series actually received some fire for the announcement that Masayuki Doi, who has done art/coloring/other work for Atlus games would be doing character art. Several Sentai plus other artists would be doing new demon art for Shin Megami Tensei IV.
MST3K Mantra - Satan is based on the Jewish view of Satan, the Quirky Miniboss Squad has the Catholic Uriel and Raphael, and only a few people will be allowed into the Millennium Kingdom in Shin Megami Tensei II, which mirrors (the Hollywood version of) Jehovah's Witness teachings. Thor, Narukami and various other thunder gods co-exist and move on.
Sequel Displacement: The series is called Shin Megami Tensei, ignoring the first two games (Digital Devil Story: Megami Tensei and Digital Devil Story: Megami Tensei II).
Before Shin Megami Tensei, there were two games for the Famicom called Megami Tensei (the first was adapted from the first novel of the Digital Devil Story series of novels). Few outside of Japan have heard of them, and even in Japan the number of gamers who came of age during the 90s and 00s who've actually played those games (or read the novel) are increasingly few in number.
Shin Megami Tensei III: Nocturne was not the first game released with the Shin Megami Tensei supertitle in the west. The largely forgotten Demi Kids games also had it (in small text) and predate Nocturne's release in the west by a year.
In a way, it does. That series of spells is named for the mountain where Armageddon will supposedly be fought.
This extends to any Almighty attack, really (the Megido are the main spells but not the only ones).
Devil Survivor takes it Up to Eleven by adding the -dyne suffix. As if Megidolaon wasn't bad enough, Bonus Boss Lucifer can drop Megidoladyne on the entire map. And did I mention that it gets 50% more powerful with each hit?
Then others like Strange Journey throws fuel on the fire by planting new spells in that are of the same type. Thought Megidolaon was awesome? Add in Big Bang which is even more powerful by a good 200 points. Then we have Babylon Goblet which has a chance to charm. Good luck recovering from that. And god forbid you get the eponymous JIHAD because not only is it one of the strongest spells in the game, but it also LOWERS THEIR STATS TOO. But to be fair while you have those, you can bet your opponent has even better shit than you.
That One Boss: Matador and Mot in Nocturne, the golden metal trio in Persona 2, Intrepid Knight in Persona 3, anyone in Digital Devil Saga with the second boss theme and probably a few more. Of course, if you don't use all of the options that are available to you like ailment inducing ammo, buff and debuff skills, buff and debuff cancelling skill, healing skills, elemental and ailments immunity to at least some of the bosses attacks, then expect lot of bosses to suddenly turn into Nintendo HardThat One Boss. You know what, let's just tell you we have ThatOneBoss/Atlus (where Shin Megami Tensei makes up most of the article) and leave it at that.
Uncanny Valley - Part of the series' aesthetic. While it remains distinctly manga, the characters tend to share the same grayish skin color and nearly all share the distinctive eye design.
This was noticeably absent in Devil Survivor and the later installments of the Persona series, both of which used a more manga, cartoony style, that severely contrasted with all the Nightmare Fuel of the game.
Both of those series had different character designers for the human characters, while keeping Kazuma Kaneko's demon/persona designs. Kaneko is responsible for the human character designs in all the main series Shin Megami Tensei games except IV, as well as DDS and the Raidou games.
Values Dissonance - The ratings for each game vary greatly by the region. Nocturne (Lucifers Call) and vanilla Persona 3 have significant gaps between the PEGI (12+ ) and ESRB (17+ ) rating alone.
Nocturne even got an A in Japan, which basically means suitable for everyone. Note that this game is considerably more difficult than the already difficult Digital Devil Saga and Persona sub-series, you get turned into a demon by having a snake-like parasite get dropped into your eyein first-person perspective and you can become the literal anti-Christ as you become the new General for the legions of Hell/Darkness to wage war against God.
Many speculate that the only reason many of the games—even the less violent ones such as Persona 3 and 4—have M-ratings in the United States is because of Mara, who is absent in Devil Survivor games, one of the few series in the franchise to carry a T-rating.