Like, I legitimately got more joy in helping those folks in the Lochs getting their salt mining up and running again or seeing the changes with the refugees in Ul'dah (which was my starting city as I chose Gladiator to begin with) then I did fighting Shinryu at the top of some "heavenly battlefield" because if you've fought one big damn dragon, you've fought them all, and by this point in the story I've murked Bahamut and Nidhogg who had substantial lore behind them, while Shinryu was "surprise final boss with no attachment" levels of *sigh* lets get this over with...
Zenos' general lameness further diminished whatever impact it was supposed to have, as well as making my victory outright confusing because this guy has been one-shotting me throughout the expansion but now I can suddenly take him on after he gets a huge power-up? Felt like I was playing a shounen anime complete with protagonist BS, which is saying a LOT considering ARR and HW had us getting helped by Hydaelyn.
Hell, my favorite section of Stormblood was the Naadam, because it was nice having this big old fight where I'm just a PIECE of the victory conditions but still needed everyone else to make it happen, and Magnai and Sadu were WAY better "rivals" than Zenos could ever hope to be. I'm not the biggest fan of Magnai overall admittedly, but still some respect there... even if I did laugh out loud at "Little Sun" later on. I also just generally liked the whole section about getting groups together to team-up to take back Doma and Ala Mhigo, because again, it's more personal and "shoulder to shoulder" with the world than being just the Eikon-slayer and "the only one who can do the thing" whatever that thing might be.
As for things I DID enjoy story-wise in Shadowbringers such things included:
Dealing with the Light Warden threats and returning the night sky, because again, I can SEE my actions are making a literal difference and bettering NPC lives. Eulmore was especially memorable because these were people that had to actually face their own follies and roll their sleeves up to make that better world happen beyond just what I contributed. (And I found the Chais precious personally.)
Seeing how competent and capable the Scions could be WITHOUT the Warrior of Light around. They may have needed me to save the First, but they were doing a fine job keeping hope alive for my arrival to matter, and some of them had been doing it for YEARS.
Il Mheg in general was one of my favorite zones in SHB if not the entire game, and I need to find out how much of those cookie and candy items in Lyhe Mheg are actual furnishing.

I'm sure some people find it an eyesore, but this stuff makes me giddy instead.
AND I NEED THE FEO UL MINION SO BADLY IT HURTS.
I was initially unsure about the whole "oh, Ardbert and his crew were actually good guys and didn't REALLY want to destroy you and the Source to save the First" thing, but they grew on me, especially after doing the Role Quests and seeing more of their lives beyond even just being crystal-bearers, and was happy to see them regain their heroism in the eyes of others who deemed them villains.
I enjoyed the Rak'tika Greatwood section of the game as well because I'm admittedly just as interested in lore scraps/in-game cultures as Y'shotla is, I had been waiting to see more Viera being involved in the plot beyond just Lyna, and who doesn't love LAHEE and SCREE?
I think the only zone and its attached story that was genuinely weak was the Tempest, partially because its the only zone I didn't really "save" (rather we ironically made things more difficult with the big old air pocket) and while the initial premise of sundered worlds and souls is interesting and unfortunate, it was hard to become outright attached to the Ancients (much less sympathetic of Emet and Elidibus) when the only fix would be continued mass genocides of more worlds and the following Calamities, or how the time period of this event takes place even beyond the ruins of lore that dot the Source and First, while also having little to see or explore of it compared to say, the Flood of Light and War of the Magi. There's a dialogue I remember having with Alisaie about Alphinaud where you can say something along the lines of "he's learned to talk 
with people instead of 
at them" and that's how I feel about the Ancients. I'm being 
lectured about why I should care, feel bad, and want to die for them and all of this is being done by pompous and selfish psychopaths. It doesn't really leave a positive impact.
I also can't say I'm the biggest fan of Hydaelyn being a primal or the implications that I might have been this "Azem" because not only does it call into question my motive for even wanting to help people (am I just a really nice tempered?), but my possible origins in general because apparently I was also one of these Ancients and I'm just a uniquely sundered soul rather than "same as everyone else" like I assumed.
And honestly, listening to Ancients talk was starting to hurt my ears...
Post-Shadowbringers being almost entirely about more Ascian scheming when I thought everything was done and dusted and I could FINALLY return home wasn't fun, or how I got stuck with the First being in a Starshower for WEEKS because I couldn't find enough people to attempt Seat of Sacrifice (even unsync) because 8 people is MANDATORY with one of them being a tank and healer due to mechanics. Hell, it took almost as long to do Dying Gasp, and in the case of both trials I spent the majority of my time dead on the floor because neither Hall of the Novice or previous fights prepared me for most of the things being thrown at me.
It really deflated a lot of the spectacle of taking down the remaining Unsundered when the fights were delayed for longer than it took to reach them, the battles themselves were annoying when finally attempted, and it's really hard to take it seriously that I "totally beat those guys" when I didn't contribute much to the actual outcome. (Also Time Maneuver Events are the devil, and one of them was legitimately hurting my hand.)
Oh, uh, right. I guess there was the stuff with Gaius and the Weapons too. Full-stop I'm not a fan of any questline that tries to make me feel sympathetic or want to pal around with Imperials beyond Cid and Maxima, especially when I don't feel like Nero or Gaius have done enough to redeem themselves for me to be giving them approving cutscene nods, or how its really REALLY hard to care about Imperial citizens getting caught up in wars of succession or experiments when there's about a 99% chance those same citizens didn't care about what was happening to the "savages" of Eorzea and beyond. Also really hard to convince me of "nuance" among Imperials when Valens was so over-the-top ridiculous, like the writers were so desperate to convince me that Gaius "wasn't so bad after all" that they needed to create an outright caricature of the kind of Imperial an Eorzean might describe (including the really uncomfortable sexual predator element).
I will say there was something strangely satisfying about making Gaius watch as I kill his "children" and he couldn't do anything about it because he had helped to create the conditions that lead them to their decisions, and how he had to watch as "Eorzean might and technology" rolled them the same way we had to watch Garlean might and technology put us on the backfoot for so long. I still wouldn't say he's fully redeemed, but at least we have an understanding of why is grandiose speech on that elevator is so boomer cringe now, lol.