Digimon Savers/WMG

Belphemon is a corrupted Metalgarurumon
Psychemon, a recolor of Gabumon, becomes Astamon. Astamon canonically evolves to Belphemon. It is said that Lillithmon is a fallen Ophanimon. Daemon is a fallen Seraphimon.

Yggdrasil is a freak mutation compiling Izzy's computer and Hypnos' machines

 * If it was Izzy's computer the whole world could be Izzy's attempt to simulate a more orderly world, hence the deeper understanding of human digimon relation. Hypnos explains why Yggdrasil tries so hard to keep humans and digimon separate.

Digisoul is Spiral Energy.
When you look at it, they are too similar. 1) It is produced by intense feelings and will to live 2) It induces evolution 3) It manifests as a colored energy 4) It can break the laws of how things should work. Furthering this WMG, Digimon Savers is actually an alternate reality version of Tengen Toppa Gurren Lagann. Masaru is a combined counterpart to both Simon and Kamina (Hot Blooded like Kamina, saves the universe like Simon), Yoshino is Yoko and the partner Digimon are Gunmen (Agumon, for example, is Lagann), with the Burst Modes being counterparts to the Tengen Toppa mechs from the Lagann Hen movie. Some, like Tohma, Ikuto and Kurata are unique to the Savers universe (unless you see Tohma as a counterpart to Rossiu). On the villainous side, Mercuremon is Lordgenome's counterpart and Yggdrasil the Anti-Spiral's.

Yggdrasil and the Royal Knights did not get involved sooner because they were killing X-Digimon.
The climax wasn't the first time Yggdrasil got fed up with the world and started over. It had been done before but the X-Digimon, who had developed an immunity to Yggdrasil, escaped from the old world into the new one. The Royal Knights were busy hunting them down. The only X Digimon we see(Metalphantomon) is hiding in a fissure. He was hiding from the Royal Knights.
 * Adding to this, Yggdrasil's horrible actions are what allowed the Seven Great Demon Lords to rebel, not because they were good or anything but because enough Digimon were willing to help them destroy Yggdrasil's new Digital World.

The Series was partially funded by the Yakuza and contains Yakuza propaganda.
Some fans theorize that the Yakuza may have had a hand in the series creation, mainly due to the frequent use of terms such as "Aniki", the overtop incompetence and corruption present in the series authority figures and the framing of delinquent characters (Masaru and Bancholeomon) as heroic figures. Since Yakuza like to use Manga and Anime as recruitment tools, some fans think that this may have been an attempt to make anti-authority organizations and individuals (and thus the Yakuza) seem more sympathetic to children in comparison to law enforcement agencies framed as corrupt.