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.
Epileptic Tree - Satan in the second game states that a "heretic is trying to destroy the world." Fans theorize that he's referring to either Aleph from Shin Megami Tensei II or the Demi-Fiend from Nocturne.
The Seraphim appearing in the second game really don't help any. Expecially since one of them - in a factory - says "This is not the factory I knew..." Guess where he was found in the second SMT game.
Brahma has something akin to the Amala Drums on the heads of his various forms. Let that sink in for a minute. Though it is confirmed inseries he is not connected to God/Great Will by Schrodinger himself.
Les Yay - Pretty blatant in regards of Argilla and Jinana. Heat even Lampshades it by complaining about how she's upset about her "girlfriend". This was due to her being forced to kill a frenzied Jinana.
Like You Would Really Do It - Averted. When you first see Roland and Argilla'sHeroic Sacrifices in the second game you'll almost certainly dismiss them as just hiding because the game still has a long way to go and, given the way you're encouraged to optimise your characters for specific roles, killing 2 of them off for real would SERIOUSLY handicap your party's effectiveness over the long term. By the time Gale and then Cielo have been far more conclusively killed off on screen it finally sinks in that, no, Anyone Can Die- as you immediately see when Serph and Sera, the last 2 characters left, die after them and the final stage of the game effectively takes place in the afterlife.
Magnificent Bastard - Jenna Angel is pretty much at the center of every important event in both games. Taken to its logical conclusion in that she is both Sera's mother and father.
Scrappy Mechanic - Berserk Mode in 2, which happens during higher numbered Solar Noise phases. You can't use magic or items and everyone becomes a Glass Cannon. The only thing you can do is use physical attacks (or Hunt skills) or wait a turn, resulting in Critical Or Death battles. Fleeing is also an option but Karma points get more than doubled if you win.
Thank god fleeing isn't just an option, but has a 100% guaranteed success rate in Berserk Mode. Also, the developers applied Fridge Logic to the idea of only being allowed to use physical attacks, so your characters ignore enemies' physical resistances and immunities, allowing them to slaughter enemies they wouldn't even be able to TOUCH with physical attacks normally.
That One Boss - Cerberus in the first game, Meganada in the sequel. If you beat Meganada, even just barely, the final boss will be cake.
Let's not forget Ananta. It gets 7 actions per turn, hits you with Dekaja, boosts itself through the roof with Tarukaja and Power Charge, and is smart enough to attack the same person constantly rather than spreading out the damage. Not to mention that it likes starting every turn by casting Sonic Wave, Stun Wave, and Dream Haze in succession. And if you even try to use a Void Physical ability, it rips of Mudo and Mudoon for every attack. No elemental weakness either.
Woolseyism - Mostly kept to name changes: the Assignments became the Vanguards, the Merrybell became the Maribel, "Mick The Nick" became "Mick The Slug", and so forth. Strangely enough, they didn't change the names during cutscenes: Gale's map of the Junkyard displays all the original names of the Tribes and Tribe leaders.
They named one of the Mantra (skill-teaching equipment) "Wikipedia" as a joke.