This is most likely the reason for the movie ending the way it did. Omegamon X using All Delete on Yggdrasil should have made it impossible for the Digital World to be restored at all. The only way the Digital World could have been restored is if Yggdrasil had already set things up for that to happen upon its demise. The only way it could have set all of that up would be if that was its goal all along, due to I Cannot Self-Terminate. It knew it was corrupting the Digital World, so it set all of this in motion, combining a Xanatos Gambit, a Thanatos Gambit, and a Zero-Approval Gambit into a single master plan. That would also make it quite The Chessmaster, come to think of it. Let's face it, this is the most logical explanation, which leads to massive Fridge Brilliance when you think about how much time and effort it would have taken to set all of this up!
To elaborate further on the Thanatos Gambit Theory, the reason it needed to destroy itself was because it was being corrupted either by some unknown outside force or the very virus it used to kill certain non-X-Antibodied Digimon in the first place. Thus it knew it was corrupted (hence the creation of the DEX-Dorugamons) and in turn corrupting the new Digital World, thus initiating the Thanatos Gambit mentioned above to solve the crisis.
"Funny Aneurysm" Moment: Seeing Omnimon/ Omegamon, the hero of Our War Game (albeit a different one than the one in this movie), destroying and brutalizing defenseless Digimon on Yggdrasil's orders can have this effect on some fans.
Adaptational Villainy: Even if these are not the same characters as their incarnations in past seasons, it still is jarring to see these very Digimon we have rooted for, such as Omegamon, Magnamon, and Andromon, act in such contrast to their original selves, not helped by the fact that apart from Omegamon, pretty much every "returning" character is voiced by their original seiyuu, as if to say these were the same characters from the previous seasons. Curiously, the one inversion to this is Mummymon, who gets a case of Adaptational Heroism, as he's clearly on the side of the heroes despite his attitude.
Karma Houdini: Omegamon got off really lightly for everything he did during the first half of the movie. Magnamon as well, as, despite doing nothing directly, nevertheless warned Yggdrasil of Omegamon and Alphamon's arrival.
Word of Dante: The Silphymon here is voiced only by Kouichi Toochika, Hawkmon's seiyuu, contributing to the idea that, for Miyako's Hawkmon in particular, Silphymon is his natural Perfect stage, not necessarily requiring Tailmon to achieve.