Like others have said, perhaps all the things that happened so far have actually flipped the script. Weiss is becoming the MC of the story now, and Allen is turning into a villain. it seems like it's kind of a yin and yang thing. Weiss, as dark as his impulses are that seem to control his brutality and etc., is actually a decent guy who wants to protect people. Allen, while a good dude initially, has some darkness in him that we saw with his backstory about wanting to obliterate all monsters due his past. And while such a desire in itself isn't bad, the manga showed him his desire to be dark and filled with an extremely vengeful hatred. He's always had that dark in him, and while the original story would have led him to become the protag, perhaps in this iteration it's actually causing his darker side to take over more. Weiss inevitably doing what he does is causing an entire reversal of the story and pushing Allen to become the villain perhaps.