Would you like to know about another villain who has no rhyme or reason to what he does? The Joker. And he is rated the number one villain of all time on many, many, many platforms (and even if he isn't, he's always top 5). While there have been many iterations and imaginations of the Joker, the main thing that drives any of them is giving the Batman a bad day. That's it.
Even if we want to stay in the FF universe, Kefka is the villain I'll turn to. One of SE's best and most memorable villains ever; also had no rhyme or reason to what he does. We only learn that he was driven mad from the mako infusion experiments. Otherwise he is just nihilist, hell bent on destroying all life because he simply cannot comprehend the purpose of it. We never got an extensive background to Kefka. As a matter of fact, we have more on Zenos than we do him.
I am not saying Zenos is a great villain like the Joker or Kefka, but what I am saying is that villains don't always need these drawn out, elaborate upcomings to be understood. But we do need to know what motivates them into action, and we have that with Zenos. If you don't like that he is a polar opposite to the WoL and arch nemesis, then I don't know what to tell you. That's what he is. To come out now with some kind of sob story where his mother abandoned him or some crap would just be silly and actually be a disservice to his character.
Zenos also finished himself off more so than just offed himself. He was already dying from his injuries sustained during the battle over the Menagerie. The true cop out, was that he made the decision to fuse himself with a primal. This right here is what I would find to be a valid reason for Zenos to fall out of favor with so many, and I've only seen a select few mention it.
In short, it doesn't surprise me that the same people who dislike Zenos strongly favor Nidhogg and Emet. They are two entirely different tropes of villain, and I find the latter to be far easier to write. I want a villain to make me hate them in a good way, not sympathize with them. Thordan, Livia, Ilberd, Lord Zephiren (the HW knight that struck down Haurchefant), and that lower than a rat brother of Yotsuyu was quickly headed in that direction as well. I HATED them. There's no sympathy, no reasoning, nothing relatable. It wasn't about stopping what they were planning to do; it was about hunting them down to serve them due justice for what they've already done. These are characters my character specifically targeted for death, and I love them for it.
If Zenos had actually killed Y'shtola at the Reach; believe me, everyone would be whistling a different tune about him now. The issue I have with Zenos is he really hasn't don't anything to make us really hate him other than hand us an arsewhooping, twice. We will see what the devs cook up, but yeah, if the devs want to make us really hate him; he is probably going to have to kill someone of great significance at some point. And they can't just bring in someone for him to kill. Haurchefant's death was so effective because his presence carried over two expansions, and he was fundamentally important to HW's story. Needs to be someone on that level.