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.
Burizalor (Freeza's Expy) definitely fits the bill. He is responsible for destroying the Northern Realm and killing many innocent lives to supplement his arrogance of being the strongest in the universe. He personally crossed the line to Taichi after he kills Sora, in which he made a grave mistake of the birth of Omega X to defeat him.
Virus (Cell's Expy) is another. Although programmed to kill, he shows no concern over feeding many human and digimon lives to increase his power, and gleefully shows the restless souls of his victims while powering up in front of BanchoLeomon, Jax, Sonja and BlackWarGreymon. He will stop nothing to absorb Artificials Jax and Sonja in order to reach his perfect form. After achieving his perfect form, he began to hold a tournament called The War Games to challenge many heroes in inspiring terror to the universe. He then crossed the line when he killed Blackwargreymon, just to make Celesta X angry. Then attempting to blow up both worlds after spitting out Jax and Sonja. And NOW he's going to destroy everything, including the solar system! Also, his future self in Dimitri's timeline (and even the main one) mention that he killed Athenamon.
Super-Reaper and Teen-Reaper are most likely to take the cake.
Stunt Casting: There are characters borrowed from other fanfic authors and contributers.
Maxacorn's D3 OCs, children of the DigiDestined, have been casted into the story since the Spira Saga. From this author's D3 series, they are highly known to transform into Ascendants, but in this story they must work to regain those powers, which they've lost in some incident in their previous world. The masked fighter, X, is also Maxacorn's character and is rumored to have been a great warrior from a parallel universe.
Also has BW, Pikkan, Digital Warlord.
The D3s, often called Magna Warriors or Digital Humans, have revealed their heritage to the kids.
The Higher Ones; Simms, Russell, Otto, and Jean play the role as the Kais.
UltraSonic007's UmbraDevimon character is exclusively from his Digimon epic Zero 2: A Revision. This villain's role has been reduced to being The Brute, but still a formidable threat to the heroes. His core being was based entirely off NeoDevimon. He was defeated in Episode 35, only to return recently in Chapter 50 to merge with his creator, Shadramon. That didn't last long as UmbraDevimon bit the dust for good in 51.
Dark Warrior has LadyMyotismon, Elfmon, IceLadyDevimon, Funkymon, KingDevimon, DarkMagimon, and D-Reaper.
What Could Have Been: Originally, the Tamers such as Takato, Henry and Rika would have appear in Season 3 as the Kai verse. Same as the Frontier Digidestined. But this has change to have these characters FROM the YYGDM universe as the roles instead.
Originally, the Xros Wars cast were suppose to appear if a planned canonical ending after Digimon Fusion Kai based on Dragonball Online, but it was scrapped. They officially appear in Across Dimensions.
Dimitri and Karin were not going to appear in Season 2.5, till they show up in the last minute.
The Devas are supposed to be revived by DarkMagimon in Season 3, but its too much, so its scrapped.
The Woobie: TK, Kari, Matt Ishida (sometimes), Ken, Dimitri Ishida