I think they always were his creations, back from when he was still a Neo Arcadian Scientist. However, they were wise, and well meaning judges. They even doubted Copy X's decisions, noting how different he had become. (they did not know of his replacement)
Their transformations were always there, as evidenced by Mantisk referencing his sickles in the drama track.
"Mantisk: And if I thought I had to take an unnecessary life with these hands...it would be a weight on my mind. Indeed, that my sickles are dull should be proof of peace."
What Weil did however, upon his return, was reprogram their brains under the guise of an "upgrade".
Cerberian: Goruruuaahhh...! Stop your whining, you little gnat! We have to prepare for Lord Vile. It doesn't matter what happens with your friends!
Harpuia: Did you say..Lord..Vile? You..what are you talking about!
Foxstar: Ohoho.. While you were lollygagging around, Lord Vile gave us an upgrade. Yes...somehow it's so refreshing..it's a good feeling! Hoohohoho...!
As for Weil himself, he was exiled from Neo Arcadia. Remember that after the Elf Wars, Neo Arcadia is pretty much the last remaining LIVABLE place on earth. Everything else was left desolate wasteland and deserts. Weil was put in that regenerative suit and exiled to forever wander the waselands he himself caused. Always regenerating from near death. Suffering, but unable to die.
Omega meanwhile, was confined to the Forbidden Ark, and launched into outer space.
I figure they did not expect Weil to actually survive and pull through. They figure his mind would just break or something and he would veg out. or something. they just didnt expect him to ever return.
However, he did return, and if Z2's ending is any indication, he went back to his old lab to derail Omega's orbit and crash the shuttle.
Since he revived Copy X, (Reploid resurrection is his specialty) Copy X ended his exile. After all, everyone obeys Copy X without question, since yknow, you dont question him. That, and X's disappearance was covered up from the public. Only the Govt knew. Harpuia stood in for X, and when he returned, I bet people were relieved. It was really all because Weil revived him that he rose to power.
He planned it ll out from the start. He put it in X's head that the big 4 had failed repeatedly, an that Weil himself was a good worker and did not fail. he knew Copy X would demote the big 3 and promote him, since he pretty much had become CX's advisor. He knew Copy X would fight Zero, and knew he would lose again, and try to trigger his Seraph mode, and as such, planted a bomb in him to detonate when he did. As such, since he was the head of the military, and the highest ranking official after the big 3's demotion, he used ordinance 8 to make himself leader.