I like this answer, because it's sort of a complete answer and a non-answer simultaneously.
With hindsight in tow, it is pretty hard to flesh it out from a, "while it was current perspective." I'm of the mind that the point of Stormblood was to do a lot of worldbuilding in a very short amount of time, with the war with Garlemald basically being the excuse for why we go globe trotting. First time leaving Eorzea and what not.
I also think that what they were striving to do with Zenos was to show us a sort of, "Luke in Palpatine's Throne Room scene" only it'd just be a Darth Vader and Luke, no Palpatine. I guess? The analogue I'm trying to describe is that in Return of the Jedi, the war with the Empire and the Second Death Star is a very pivotal thing for the galaxy, but it's juxtaposed against the personal conflict for Luke. The way the battle goes for the rebels fluctuates along similar lines to Luke's confrontation with the Emperor. I.E. The real battle is good vs. evil, and the personal battle is what's directing the battle outside. Of course, that's not what's actually happening in universe, but it's what's happening with the script.
How I relate this to Stormblood is in the fact that when we do face down Zenos, he now knows more about our own gift and how to use it than we do. Since they can't have quite the same personal dynamic, nor the real isolation of the Emperor's Throne room scene, they resorted to a very direct showing that our real enemy is our old enemy, primals. Primals brought about by the Ascians. It's also because there's been no real overarching explanation on the Echo as with The Force, and we've had no mentor or master with directive for it. I'm just saying it's treading somewhat similar grounds to the RoJ thing mentioned before.
Bear with me. Every patch during Stormblood ends with tying Ascians and Primals and the special world back into FFXIV. Simply casting down an Empire is a fairly tired trope, so they want to keep us in feeling special while also delivering an original. The ultimate point of Stormblood is that we take war to the Garleans, but we find out they were puppets to the Ascians all along.
A major theme of Stormblood was liberation, and the way I see it, they wrote Zenos into the story as a way to liberate themselves as writers and destroy the empire so that they wouldn't have to stick with that trope.
Heh, I sound like I'm reaching to myself.
Anyway, as an aside, it's actually sort of a trope in itself, because it's usually what happens to empires in Final Fantasies. The Empire is destroyed or beaten somehow at a middle/late point in the story, and then the real threat rears its ugly head. We could scrap what I just spent 45 minutes pulling out of my dumper, and say that this was the point of Stormblood. To show the Empire is beatable, and then have them casted aside by a greater force.
This happens in FFII, FFVI, FFVII(hey Shinra maybe an Electric Company... but... Business Empire), and now in FFXIV. Maybe I missed one? Anyway, in FFII, the Emperor is killed, and the Empire is pronounced defeated, but then the Dark Knight takes over and resumes the war only for SURPRISE HELL EMPEROR!
In FFVI you engage the Gestahlian Empire across many different skirmishes, from Doma to Narshe to Vector itself. You turn to the Espers in desperation, and they ransack the imperial capital. The Empire sues for peace, but then shows their true colors and raise the floating continent, and you engage with their air force. Once you're there, it seems like it's the end of the game, and you're going to have to stop the Emperor and Kefka somehow... Only for Kefka to betray the Emperor, cast down the Empire entirely, and destroy it, and the world, leading into the World of Ruin arc. You never actually get to engage the Emperor himself in combat in FFVI.
FFVII has it happen pretty early. You invade the Shinra HQ, and you likely know the details of it better than I do, but your attempts at stopping Shinra are foiled, but while you're in prison the real bad guy swoops in and kills Shinra himself along with most all of the building personnel. After that, Shinra's still around, but you know they aren't the biggest threat, even though they're 100% responsible for Sephiroth being who he is.