the entire viltrum becoming good overnight after spending a few months on earth
we, as an audience, were made believe that the viltrumites were this group of horrendous and bloodthirsty monsters who have spent most of their existence conquering planets and destroying the ones that didn't obey their rule, but then the next time we see them after the viltrumite war arc, ALL (minus thragg) of them suddenly became attached to their families.
this really undermines the message and development of nolan's arc, as the whole point was to show that deradicalization is incredibly difficult, and how more often than not, people can't let go of the ideals they were conditioned to believe, going as far as to try to kill his own son in an attempt to deny himself the chance of becoming a "traitor"
like, this whole process took decades, and you're telling me that these guys just managed to do it in a few months?