This is a "Wild Mass Guess" entry, where we pull out all the sanity stops on theorizing. The regular entry on this topic is elsewhere. Please see this programme note.
Shin Megami Tensei IV
Someone tampered with the past similar to Raidou Kuzunoha vs. The Soulless Army, which might explain the anachronistic nature of East Mikado.
Jossed. Mikado was simply built with God's Chosen (kidnapped children who don't remember Tokyo) on a ark and was built on the ceiling of Tokyo afterwards. The flow of time is different between the two.
The characters are in some kind of time loop or their future selves are contacting Flynn to convince him to take the side they want.
This game takes place after SMT2 on the main timeline, somewhere around the year 3080.
Jossed. Characters mention China and the United States also having come under demonic invasion. Neither country exists after SMT1.
Can evidence of the latter be provided?
Only anecdotally: The Great Flood in the closing act of SMT 1 drowns the entirety of Tokyo save the Cathedral. Given how high the water would have to rise to do so, it's not much of a stretch to guess that almost the entire world found itself underwater, except without a convenient Ark.
According to SMT2's manual, only Tokyo (with the exception of the Cathedral) was flooded. Other than that, the point still stands; China and the US would have presumably been too damaged to rebuild.
Jossed further. There is evidence in the game (mentioned at Kasumigaseki's supercomputer, which surprisingly still functions) saying the game takes place in (irony ahead) 2038.
God/YHVH has decided, since the Schwarzelt and Demi-fiend failed, to just take his chosen and create a paradise for them.
Jossed. Most of the game's plot is caused by The White, manifestations of human despair at God's ultimate control over mankind's fate. Their goal is to remove mankind from the control of god by ending existence. Where Strange Journey falls in relationship to this game is unclear, but Nocturne is clearly unrelated. Besides, Strange Journey is a textbook example of Gaia's Vengeance, while Nocturne is one link in an inconceivably large Thirty Xanatos Pileup between the Great Will and Lucifer (or its resolution, depending on your choice of ending).
Strange Journey has no relation to the game as the Counter-Demon Force Base has info that reveals that Country A created the Demonica to fight demons, which people didn't know about in Strange Journey until after they entered the Scharzwalt. Japan became the world's second best demon fighting force using the armor.
Furthermore, if the neutral ending is the canon one and assuming that Gore wasn't lying (which is unlikely), mankind picks itself back up and grows to be prosperous without intervention.
Not entirely jossed, it's revealed by both Merkabah and Lucifer that as long as humans cling to God or have desires respectively that the cycle of law vs chaos will continue indefinitely, so even if the protagonist in SJ gets the Schwartzwelt nuked in the end it will come back too as long as humans abuse nature. Couple that with how Mastema talks about how he slaughtered Unclean Ones before, Demonee-ho, and the Demonicas themselves being in Tokyo. What better way for a person to fight demons with a suit that enhances you? Even though they are the prototype models, Jack's Squad shown how powerful they can be. Finally, it's revealed that it is possible for Demons to come out of the Schwartzwelt. Even if it's nuked, it is unknown how many demons escaped, meaning it's entirely possible the events of SJ caused what happened in IV.
All the demons disappear in the Neutral Ending when the Schwartzwelt disappears. It's also stated that the Demonicas were specifically made to combat Demons, which the ones in SJ weren't made for such a thing. IV's also lack the adaptability that the Demonicas in SJ had. Demonee-ho is also most likely a different demon much like how there are different King and Black Frosts. Mastema was talking about literal biblical times when he spoke of slaughtering Unlcean Ones and it's unknown whether he was being serious or not since the whole fight was a joke. Also, different technology exists in the different alternate worlds and some technology gets developed in multiple ones, which explains the Demonicas, as well as there being countless multiple worlds out there, which the Yamato Perpetual Reactor can access through the Expanse.
Honestly this will forever be a mystery. There are valid points on both ends. One could just point to how Nocturne reveals how the series is not on one particular universe but over multiple universes. There's just an equal of a chance as SJ causing IV's plot as there is of SJ having nothing to do with it at all. This is backed up by how depending on where you get SJ, in American releases the protagonist is American. Now this screws up lore a little bit considering it's implied that America and China at least are in ruins. No one knows for sure. All we can confirm is that Flynn is the fifth one to step up to the plate where SMT I's protag, Hawke, Demi-Fiend, and SJ's protag came before. They all had a say in the fate of everything regardless on what universe they are in.
This game takes place during SMT1.
Specifically during the 30 year gap between when the nukes fell and when Kazuya & co are in Makai. It is mentioned that it the nukes fell 25 years ago meaning this would take place 5 years before the second part.
The details of the main endings make this HIGHLY unlikely.
The Yamato Reactor is somehow connected to the Amala Network.
Unlikely, given that the Yamato Perpetual Reactor is actually a particle accelerator..
Isabeau is this world's incarnation of the Heroine from SMT1.
Alternatively, everyone is a reincarnation of the cast of SMT1.
We know Flynn is a reincarnation of someone who gave his life to raise the firmament. That someone might have been the Shin Megami Tensei I protagonist, in an alternate version of the events of first game of the series. The Law and Chaos protagonists likely existed as well, but died after Tokyo was saved from the ICB Ms. The Heroine likely met this fate as well. 1500 years later, they were reborn as Flynn, Isabeau, Jonathan, and Walter.
Time doesn't move faster for the people of Mikado. Time in Tokyo moves slower.
The Yamato Reactor generates black holes. Black holes cause time dilation. The Eastern Kingdom of Mikado hasn't experienced 1500 years of history while only 25 years have passed in Tokyo - 1500 years have passed in the outside world while Tokyo has experienced only 25.
There might be some evidence to this. When Masakado destroys the barrier and assumes his true form and from pretty much you see in Mikado, the outside world is filled with greenery and lakes. If the entire world was nuked over, it's doubtful it could recover in only 25 years time.
Furthermore, it was more than 1500 years outside - the calendar kept by Mikado started with the kingdom's foundation by Aquila, and he (as the local Akira) and the remains of the Counter-Demon Force already had worked for some time to drill the path that would become Naraku to the surface. Furthermore, the Minotaur claims it's been more than 1,500 years since he was posted at the Hall.
Navarre's parents were among those killed in The Purge.
When you eventually pick up Navarre at Kiccigiorgi, he's dressed in common clothes and is clearly disheveled from being pursued by the angels. Most likely, after being discharged, he was taken to his family's residence, where he more or less witnessed his family's death at the hands of the angels. He was still marked for death for possessing forbidden knowledge, and was thus forced to run and hide at Kiccigiorgi, making him even crazier after the Alraune incident and reducing him to a pauper.
He manipulates time in a very limited fashion with Guardian's Eye; he used a massively larger form of the same technique to entrap Tokyo in a bubble of slowed time to allow it to last enough for help to come from outside.