Personally in complete disagreement with the seemingly majority in this thread. Zenos isn't supposed to be an "in-lore" likeable character. He's not the WoL's friend, or really similar in many ways at all. But to ZENOS, the WoL is the ONLY person in the universe that he can relate to.
His presence in the end is wholly appropriate: despite how ridiculous it may seem to a normal person with many interests and reasons to live and find happiness, Zenos's one reason to live was to find and fight the strongest opponent he could find. And he did so with a ludicrous and frankly impressive drive. His one dimensional personality and drive made him the perfect foil not to the WoL, but to despair itself. Because he simply doesn't give a shit about anything but getting what he wants - there's no distractions or tragedies that can put him down.
And in the end, he gets what he wants, as villains sometimes do. (See Ilberd and the reclamation of Ala Mhigo) I see some people lamenting the fact that they could not deny Zenos his duel, but honestly I can't see a single reason the WoL would do that other than purely out of spite for Zenos, and spite is not a character trait the WoL has ever shown, whether you agree with that trait or not. It would be completely out of character for the WoL to not defeat Zenos when he finally becomes the biggest threat to peace and stability. The fact that you're giving him what he wants is irrelevant - the WoL does not live and fight to spite villains, they live and fight to make the world a better place.
This is why Zenos's revelation prompted by Alisae is so important. Because it prompts him to actually think about *why* we would fight him. He tried angering us, he tried hurting our friends, and he tried destroying the world, and none of it worked because the WoL isn't a character that can be taunted and driven into an irrational rage by their enemy. In the end, Zenos's solution was simply to become the one and only final loose end to wrap up our story.
I do think the ending works better when you're a player who does see their time in Eorzea as an adventure - one in which the pleasure of adventuring and challenging yourself is it's own reward, and I'd say this is actually the vast majority of players. But it does still work for those who see their adventure as simply the path to peace so they can go back to fishing or whatever without the world ending.
I feel like a lot of people simply don't care for Zenos as a character and are using that opinion to criticise his involvement in the ending, rather than criticising the quality of the writing itself. Personally, I thought Zenos was a complete disappointment in SB and didn't earn his place as a villain on the WoL's level at all, especially because of how he finished himself off. But in EW, even if in the end he didn't end up doing a whole lot plot-wise due to being manipulated by Fandaniel, his arc did come to a satisfying end.