The Plot: I'm just going to cover the overall premise of the movie and not much into details. Long ago Hoopa Unbound appeared to a desert village (later to become Dahara City where the movie takes place) an in exchange for food it opened up portals of treasure making them rich. The village asked how strong Hoopa Unbound was and so it began summoning Pokemon to battle but got so out of hand it began summoning Legendaries to battle which caused utter chaos. Hoopa Unbound's power was sealed away within the Prison Bottle until it could learn to be responsible with it, being overseen by a family who somehow have mastery over the powers of Arceus. Year later a boy part of that family goes seeking the Prison Bottle but gets possessed by it.
Meanwhile Ash & co. who, after some portal shenanigans, meet with Hoopa and a girl part of that family. Boy comes back and releases the Prison Bottle but something evil overtakes Hoopa and the power needs to be put back into the bottle. Its discovered the power within the bottle has become angry for being sealed away and now wants its freedom to become the real Hoopa. Team Rocket released the power and though Hoopa fought it off the power turns into a shadow version of Hoopa Unbound. The Prison Bottle is also destroyed so while Ash & Hoopa are distracting/running away from Hoopa Unbound everyone else goes to build another Prison Bottle. Hoopa Unbound and Hoopa Confined summon a whole batch of Legendaries to fight each other with also. Anyway they make the Prison Bottle but Hoopa Unbound is too strong so Hoopa Confined has to confront it and calm it down allowing Hoopa to take control of it. However all the Legend summoning did something and caused a tornado of doom to surround them and start closing in. Using Hoopa's portals they transport everyone to safety except the boy caretaker and Hoopa (BTW Hoopa can't go through its own rings, for some reason). Just before being erased/destroyed/crushed the closing in stops as Arceus appears to be a dues ex machina. Hoopa learns the true meaning of friendship and is able to go through its rings along with the boy caretaker. Hoopa teleports every Legendary home and it and its caretakers says bye to Ash & co. having helped Hoopa regain and control its Unbound power.
As you can tell its kind of a mess and its rushed through. Well, anything important is rushed through, when they're goofing around they have plenty of time for that. I think the words that best describe the plot is "missed opportunity". Instead of staying in Dahara City for the entire movie we could have teleported all over the Pokemon world (and along the way met/summoned Legendaries). But nope, instead we stay in one location and they just summon a whole bunch of Legendaries because in ORAS that's how you meet most of the Legendaries, via Hoopa's rings.
Not to mention the backbone of the story could have used some work. The setting makes sense since Hoopa is a genie and its overall not a bad idea but I feel like they hadn't gotten to the "why is this like the what it is?" part of story making when they were told to wrap it up and start making the movie. You'll know what I mean as I go to my other points (which aren't as long as this one).
Hoopa's Strength: I have to call BS on the power that Hoopa Unbound has. We see it take on multiple mascot Legendaries at a time yet winning (to be fair it never beats them, rather pushing them back through a portal, but its seen taking multiples blasts yet not being phased by it). Like in the beginning of the movie it takes on Groudon & Kyogre and then Reshiram, Zekrom, & Regigigas who all blast it yet when the smoke clears its a-okay and uses a Dark Pulse to shoot them back through its rings, them looking like they took a big hit (to be fair to Groudon & Kyogre they had their attacks redirected to one another by Hoopa-U). Then before the "Clash of Ages", when Hoopa Unbound was just looking around for Ash & Hoopa Confined, Hoopa-C had summon a Lugia which keeps on Brave Birding Hoopa-U which looks like it hurt it but not really as it ignores it until just before the Clash of Ages where it portals it away (BTW, Lugia doesn't participate in the big clash, because trailers always lie for Pokemon movies). I'm also pretty such it probably took a few attacks from MEGA Rayquaza yet wasn't phased by it.
I get it, you want to show Hoopa-U as a powerful Pokemon... but quite honestly it would get creamed by the Legendaries it's battling against. Also it takes control of several Legendaries including 3 which are essentially deities and the Primals? And if they can summon as many Legendaries as they want why did they stop at the number they did? But that's for another complaint point.
Arceus Power: Wait, how can this family control Arceus's power (especially when in a previous movie we met characters who literally had pieces of Arceus yet at best they could only communicate with Pokemon)? It also feels completely unneeded except to justify Arceus appearing at the end of the movie.
Ring Trick: So a crux of this movie is Hoopa can't go through its own rings (yet it can stick its hands through no problem...) which is why the caretakers decide to go get the Prison Bottle to releases it true power. Okay, fine. So at the end of the movie they're getting everyone caught in the tornado out by having the now controlled Hoopa-U power portal everyone to safety until it's just Ash & co., the caretakers, and Hoopa left. But despite Hoopa having its full power it STILL can't go through its rings. What?! In the end it has to learn the true meaning of friendship and that somehow allows it to get through its rings.
If I had to guess maybe they did this to explain why we aren't teleporting around the world... which is still stupid as this is a problem only created by the writers. Oh, and when Hoopa-U first appeared at the beginning of the movie to the village it did so by hoping through its portal ring so it's not like we didn't see Hoopa-U do that before.
What Continuity: So for the most part I can sort of see why continuity with Ash knowing most of these Legendaries isn't that important as Ash and the Legendaries who are one of kind don't really interact that much. But still there are other moments where you question things. Like Hoopa-C summons a whole bunch of Pikachu which isn't odd a first... but then we see the whole group of Cosplay Pikachu! So, are all these Pikachu actually Frank's? Also when Hoopa's caretakers show them the arc of Arceus its Clemont who recognizes it while Ash stays quite the entire time except to act amazed like he never heard of Arceus before.
I get anime writers, you don't like continuity (maybe you should have thought about that before making Ash the permanent star of the show, hmm)... but if you don't want continuity don't open up holes where you can! For example, Arcues didn't need to be in this movie. Arceus is not one of the Pokemon who appears through Hoopa's rings neither in ORAS or in the movie. Yet you shoved him in there because... because.
Evil Hoopa-U: So why is Hoopa-U evil? Actually correction, why is the power of Hoopa-U evil? Is the power a consciousness of its own? They sort of brought that up in the movie but don't really answer it besides saying it and Hoopa-C are one and the same. So what, was part of Hoopa's consciousness also sealed away? Because the way Hoopa-C calmed Hoopa-U was by showing it the happy memories it had experienced throughout the years and that somehow works. Why would it care if Hoopa-C had happy memories when it was still trapped in a bottle so didn't experience them itself? It feels like this is an incomplete idea, like part of Hoopa's consciousness was trapped or maybe the power was too corrupting and Hoopa was suppose to somehow split itself thus creating the two Hoopa (think how Majin Buu form Dragon Ball Z split himself). But they didn't have time to flesh this idea out so sort of combined what they had.
Fire, Ground, & Water: BTW found out why the event Arceus (which we didn't get...) has Blast Burn, Hydro Cannon, and Earth Power. Well, we knew it was another ORAS tie-in, but it's also referenced in the movie. To make a new Prison Bottle they need Fire, Ground, and Water because the represent the earth or something like that. It's still an ORAS tie-in and a rather hammered in one. I'd also like to remind you all that Groudon and Kyogre are just bit players in this movie.
All The Legendaries: So the main draw of this movie was the clash of ages, that big battle between Legendaries, yet it's missing several notable Legendaries. Just going by mascots, Ho-Oh didn't appear at all during the movie, Lugia was sent back through a portal before the clash began, and we saw Reshiram and Zekrom (and Regigigas) but they weren't summoned for the clash. Like if you're going to do this clash thing haphazardly at least go all out! Like the 580 trios and cute mascots would probably be too much but what Mewtwo, Deoxys, Darkrai, Cresselia, Heatran, Forces of Nature, and Gensect. Oh, and a little two Legendaries you might have heard of, YVELTAL AND XERNEAS! You didn't even have the mascot Legendaries of THIS generation? Oh wait, I forgot, ORAS. Well, to an extent, Deoxys, Cresselia, Heatran, and the Forces of Nature were in ORAS (but not Arceus yet he showed up) but I think by now I think I've shown the writers have no clue what they were doing.
Had they gone world hoping not only could they have encountered these Legendaries but other's too like the 580 Trios and the cute Legendaries and it would all make sense (or somewhat more sense).
Also, why Lugia, the Eon Duo, and Rayqauza agree to help Ash & Hoopa-C? Especially Rayquaza who previous times we saw it went into a rage. This movie actually made all the Legendaries not named Hoopa look like chumps. Heck, when the good Legendaries Mega Evolved only Kyurem changed Formes to match, Giratina could have reverted to its Origin Forme but didn't.
Empty Destruction: So the Legendaries are in a middle of city and are just wrecking it. Surely hundreds are being killed as building are being blasted and slice to bits and there should be panicking the streets as everyone tries to flee from the city... too bad the city is empty. No, that's not a plot point, the city is suppose to be inhabited, infact we even see people on the street looking up at a Legendary launching an attack going "what?". No citizen of this city seemed affected by this thus the destruction of the city feels hollow and has no weight. You're not showing anyone is in danger so what am I suppose to feel when they're destroying buildings willy-nilly?
Suddenly Mega Evolution: Ignoring that Groudon and Kyogre are in their Primal Forms when summoned by Hoopa-U, somehow when battling the possessed Legendaries the Eon Duo and Rayquaza all Mega Evolve (because of ORAS, BTW Ash & Hoopa are flying on the back of the Eon Duo... because ORAS). Now I guess this does explain a bit better how those 3 can taken on 6 other Legendaries, but still how did they Mega Evolve? Can Legendaries just Mega Evolve when they choose to in the anime?
Sitting Around Watching The End: So in the end they forces some drama by having a tornado of destruction start wrecking things because they summoned too many Legendaries (a similar plot point which was sorta done better in Life Is Strange). They say its a time-space collapsing thing... which would be a big problem if they DIDN'T HAVE DIALGA AND PALKIA RIGHT THERE! Oh, Dialga and Palkia try to do something but for some reason their power doesn't work so them and the other Legendaries are just sitting there at the end of the movie doing nothing as destruction is happening before them. You're Legendaries, DO SOMETHING!