Digimon Frontier/WMG

Some Digimon have connections with human gods/goddesses.
After all, Crusadermon has an attack named after Athena, and Nefertimon has an attack named for Isis.
 * Well, the Digital World and it's inhabitants were created from data in the human world, so it stands to reason that myths, legends, and even popular culture might have gotten caught up in the mix. Crusadermon and Nefertimon aren't the only examples of this; there's also Lucemon, the Four Digimon Sovereigns, Dragomon, Cho-Hakkaimon, and even Etemon are just the tip of the digital iceberg.

Kouji and Kouichi are really the same person.
This is one I've seen around, where they discover they are truly halves to a whole and combine to become one. Not creepy at all....
 * Rhodoknightmon (or Crusadermon, if you prefer) thought that they should "become one" in another way...

The four lost kids would be chosen to be the wielders of the four other element spirits, if these weren't intercepted by Lucemon and his lackeys.
There's no other reason on why they should be there, and why they had personalities that briefly matched the missing spirits.
 * There's a fan theory that they actually did and were mind-controlled by Cherubimon.

The reason Kouji is noted to experience more pain during his Beast Spirit transformation as well as when de-transforming is because he is picking up on Kouichi's pain.
When you think about it, digivolving in Frontier involves pretty much layering a new spirit made of data (and therefore, according to the laws of the digital world, a new physical form) over your own. This would bring you (for the moment in happens in the very least) much closer to the spirital relm than normal. Since twins are noted, in both fiction and real life, to have a sort of mental link whether they were raised together or not, it is entirely plausible that this temporary shift away from the usual physical bounds would cause Kouji to pick up on Kouichi's physical pain from his fall (and later, his mental anguish at being, well, dead and brainwashed). To further support this, if you look you'll notice that when the others are affected by their transformations it's generally in the form of being out of breath and tired. The first two times he changes back, Kouji is shown at least twice to be clutching his chest. As the first happens within roughly the first few hours of being in the digital world and the second the next day, when you allow for the usual bit of digital world-real world time dissonance this could eaisly match up with Kouichi's fall and then the defibrillators used on him and/or his death (time loop stability aside).
 * Except that, in the ending, it's revealed that Kouichi isn't dead. However, if you substitute "dying" for "falling into a coma", it still works.
 * Not even. In the first episode, the kids left for the Digital World at 6:00 PM. In the last episode, they return to Shibuya Station at 6:11 the same day they left. Not even fifteen minutes have passed since Kouichi fell.

Snimon is Myotismon reincarnated.
Just listen to his voice in the dub. Not only does he have Myotismon's voice, but even his sadistic personality. "Snimon: Now I shall destroy all your little friends one by one!"

Shamanmon actually predicted the Koichi arc.
"Shamanmon: You will come up against a foe you have faced before (Gigasmon), but this foe has a friend (Duskmon) and in beating him (Velgemon arc) you will find a friend is your foe (Koichi)."

Mercuremon's minions were fake Digimon.
None of them release a Digi Egg upon being defeated.

The ancient warriors sacrificed themselves because they were going to die anyway.
In V-Tamer 01 it's said Ancient Digimon's short lifespans caused them to go extinct. While this rule isn't always followed there isn't any evidence of Frontier not following it. When the ancient warriors saw the destruction new Digimon like Lucemon could bring they decided to give up their bodies and live on inspirit, to protect future generations. Human hosts were chosen because giving the spirits to other Digimon would curse them with short lifespans too. Humans are immune to the side effects because we age through cell division and think with our brains, not through overwrites.

The other evil spirits were corrupted, not just Kouchi's
They barely look anything like the Ancient Warriors.
 * With the exception of Mercurymon and AncientWisemon, that is. However, also note that AncientMegatheriumon doesn't look much like Kumamon at all.