Some important characters are meant to be disliked, though. You're meant to hate Thanos but he's arguable the most important character from Phase 2 and 3; you're meant to hate Hojo but he's arguably one of the most important characters in FF7, Kuja in FF9, Emperor friggin Mateus in FF2. Antagonists are antagonists because they set the plot in motion, and sometimes you can understand an antagonist's motivation while disliking or even hating them.

I have many issues with Emet, but probably the bigger one in EW is when tells the most tone deaf and hypocritical thing to the worst person possible at the worst time. "Who are you to decide whether we live or die?" to the head of a facility tasked with creating and ending new life... in said facility... granted, Emet's a huge hypocrite in general.