When Palmon evolved into Ponchomon against Etemon and Volcamon. Normally, it's an Armor form that Patamon takes with the Digimental of Purity, while Digimentals haven't proven to exist in this universe. And while this transformation can be seen as "duking it out against two prolific Musical Assassins turning Palmon into a Dance Battler", she also evolved during a surge that was affecting the group's Digivices. And who was Palmon's flower holding when she evolved? Patamon, who's already demonstrated the ability to naturally reach his own Armor evolution. As a side note, the fact that Ponchomon has More Teeth than the Osmond Family makes a lot more sense when you realize that Tokomon, Patamon's In-Training form, is rather infamous for this trait.
With the info presented in episode 46, it gives another context as to SkullKnightmon requested Devimon for dark evolution power from Millenniummon’s crystal, and AxeKnightmon saving NeoDevimon. The reason: Devimon is Angemon's manifested darkness while SkullKnightmon was a corrupted Angewomon, Angemon's ally among the Celestial Digimon.
During the battle with DanDevimon, when MetalGreymon becomes the incomplete Machindramon, some of his attacks look odd at first. Namely, he pins down DanDevimon, and instead of biting or going for a lethal blow, he starts sort-of... bashing the enemy's head from side to side using his snout. It doesn't make a lot of sense, until you remember that DanDevimon ate Taichi alive. Machinedramon is trying to force him to spit Taichi back out, the only instinctive way he can think of in his berserk state.
Millenniumon's plan to regain his body through the Digi-Destineds' Digimon partners is a case of Pragmatic Villainy. It makes perfect sense for him to first take the body of someone who actually stood against him (Gatomon/AxeKnightmon) and then resort to having Sakakkumon assimilate the data of the Digi-Destineds' heavy hitters (Greymon, MetalGreymon, Garurumon, Kabuterimon, Angemon, Devimon) and create a copy of Machinedramon from Agumon's data. As Agumon and Gabumon were components of Omnimon, the Digimon that defeated it, Millenniumon was attempting to acquire a similar power through their data. It would also explained why Sakakkumon's Chimeramon form is white.
Some of the past opponents either created by or enhanced by Negamon foreshadow it and its evolutions, Kuzurumon and Abaddomon. In addition, a few major foes not known to be enhanced by Negamon also hint at aspects of the final battle.
The Algomon are a justified case in being Negamon's creations.
Both Ghoulmon / Soundbirdmon have a single eye on their faces like Negamon.
Eyesmon is a large black creature with a numerous number of red eyes, like Abaddomon.
RareRaremon is a big pulsating blue thing with a huge mouth sporting large square teeth, just like Kuzurumon.
Sakkakumon devours everything, has rather pronounced eyes and sports a distinct Slasher Smile like both Kuzurumon and Abaddomon.
Burpmon can switch between a single eye and a face with a mouth, just like Kuzurumon.
SkullBaluchimon is corrupted into hating life and wants to put an end to the cycle of regeneration, like Negamon and especially Abaddomon.
NeoDevimon has six bulging eyes and was obsessed with corrupting Angemon. DanDevimon was a laughing mindless beast that continually smashed everything, just like Kuzurumon.
Throughout the series, we have seen various armor level Digimon walking about, despite the fact that in the original continuity, armor digivolution wouldn't be introduced until the sequel series. However, in 02, Azulongmon stated that armor digivolution was an ancient form of digivolving. So in this continuity, Digimon using armor digivolution is still a common practice.
Omegamon Alter-S easily overpowering Abaddomon, when base form was mostly evenly matched with it, may make it seem like a straight-up Super Mode, until one considers the context: Abaddomon spent the entire series collecting data, so it knew all about WarGreymon's and MetalGarurumon's powers and abilities, and it even witnessed Omegamon's two earlier appearences. The fact that it's core mimics Omegamon's Sword and Gun arms is proof that it came prepared for the fight. BlitzGreymon and CresGarurumon on the other hand, both only appeared once, against enemes independent from Abaddomon, and Alter-S was a completely newly unlocked Mode Change. It's not that Alter-S is stronger than normal Omegamon. Abaddomon just didn't know how to fight this new version.
