>>44053548The setting has already been called into question multiple times. Fairy, Steel, Dark, and abilities retroactively changing several Pokemon and moves? Mega Evolution retroactively appearing in Hoenn and Kanto?
I'm sure no one would care if someone went "yeah the reason why Giovanni and Cyrus never tried to kill you directly is because they have principles" or some nonsense. Instead, we got Ghetsis introducing the element of 'villain tries to kill protagonist' that led to horribly written attempts at compromises between serious and kid-friendly like Lysandre and Rose.
The series has shit like parallel universes and barely has anything resembling a canon, you can make excuses for 'calling the entire setting into question' if it bothers you that much.