Full analysis of Z-A's plot, both the good and the bad, which I'm probably gonna spend too long on.

Let's start with the good stuff.
(most of) the cast: Team MZ is such a close-knit group, being watched over by AZ. Lida's moods and energy would keep making me smile, not to mention her dances are funny. Naveen seems a bit pessimistic and keeping to himself, but it's amazing when his heart shows. Taunie seems like just a big bundle of energy 24/7, but she's so much more- a leader, a helper, a rival, a friend, and a hero in her own right. AZ is tall and stoic, but he's not cold- he's kind, he likes watching energetic kids doing something crazy. He deserved the every bit and more of the happiness at the end of his 3000+ year life. Canari is a total wildcard, and she's secretly kinda soft under her snarky defense system. Ivor is a lovable fool, following what he thinks is right, and no mortal can take a blow from THAT fist. Gwynn is an awkward girl who's tired of her massive, loud brother, when she just wants some peace that she found which ghosts. Corbeau isn't a villain, but I can't call him a hero either- he's sort of like an antihero. Only antiheroes I can remember Pokémon ever having are Gladion and maybe N. L is like a piece of the past, trying to blindly grope his way to the present day and then to a better future.
Mega Evolution: Wow. I love seeing all these new Megas, not to mention Rouge Mega Evolution. Mega Evolution was portrayed as a very powerful transformation, but still a game mechanic.
Rouge Mega Evolution: I love it. It makes me very motivated to win, knowing that the Mega Power might tear them apart otherwise. The battles were intense, and gave an actual REASON to have a dodge button, which Acreus never did- I just used dodge in Acreus as a speedy travel method.
The Z-A Royale: a nightly tournament for trainers in the Pokémon world is going to attract a LOT of strong trainers- which is exactly what Q Inc wanted. I'll hand it to them that they're smart, there's that. And then the top prize, a wish for the city, so long as they can grant it- you spend parts of the game wondering what you could wish for.
Wild Zone Dilemmas: The first one that comes to mind is Get Well, Fennekin, but a lot of side quests focused on the problems Wild Zones are causing for the city, but also the benefits. Are keeping Pokémon trapped in Wild Zones REALLY living with them? Should we have Wild Zones at all? Can people and Pokémon really live this close together in real harmony?
Taunie: Yes, I'm giving her a whole section. She ties Hop for my favorite rival. First of all- there's an actual reason she's around all the time- she lives in the same hotel as you. Second- the fist bump and her other jokes are great. She feels like she's the type to try to be anyone's friend, even if they told her they didn't want to be. She gets stressed and makes mistakes that she blames herself for. Lastly, which is probably my favorite aspect of Taunie's line- she starts getting JEALOUS of the player. She's the leader of Team MZ, but the secret weapon is pushing his way into that spot. They're looking toward him for directions instead of her. Who's going to be the strongest Mega Evolution user? Lida defaults to saying the player. You can see Taunie stressing her leadership and putting herself in charge more and more, until finally she snaps and wants to battle over using Floette, to prove SHE'S the leader, SHE's the 'hero' of the story. And she finally gets to be, in her own way.
Returning to Hotel Z every day: It feels so homey. Every day the city is the same and yet it's ever changing. I liked that a lot.

Now that all the good stuff has been said, I'm gonna give some criticizing.

No Villain: I might be missing some point you were trying to make, Nintendo, but the sheer lack of a villain to be angry at leaves a real gap. Corbeau was the 'fake-out' that he wasn't that I saw coming a mile away. Q Inc were building up being so suspicious, then just nothing. Like, come on.
Emma: I feel like she gets way too little attention in the plot. She introduces you to side quests, gets some appearances, but in general appears too little. More of the game should have lead to her.
Ange: Ange feels too under explained. It's a massive machine, built by AZ, the counterpart to the ultimate weapon. But it's not very well explained its link to Floette, the Floettite, or things in general. I was left confused as to just what Ange really is.
Zygarde: he just kinda pops up throughout the story and battles occasionally until he goes big guy mode at the end, pebble becomes Zygardite (who didn't see that move coming), then Kaboom, you saved Lumiose with Zygarde. But it's never explained WHY he came exactly, I guessed it was the Wild Zones but I think they should have really SAID that. Feels like he's just kind of missing out on a lot of really cool plot potential.

That's pretty much it for right-out positives and negatives. It was a pretty good game. Nice job, Nintendo. Please do this good or better on Gen 10 too.