Put the little Hoopa in the bottle also, I say. He does some pretty nasty things to them, yet they seem to find him endearing. Also, I found the mischievous little Hoopa extremely annoying and never understood the various characters' attachment to him.
Barza explains the giant form as "the Fury, the true form of the power that's trying to control Hoopa." He goes on to say that it's "a shadow of Hoopa" and that "the anger is trying to become the real Hoopa." So how is it able to take physical form and lift up huge buildings and smash them? Granted, abstract concepts like this are at the heart of the whole Pokémon franchise and it's futile to seek logical explanations, but in order to suspend my disbelief and accept something like this, I needed a more inventive explanation.
For one thing, I never quite grasped why Hoopa came in two separate forms, with giant Hoopa able to exist outside of little Hoopa. I had two major problems with this scenario. The battles are spectacularly designed and rendered and would have been much more exciting in the service of a more engaging story. The ensuing battle royale in the skies over the sprawling nighttime skyline of high-rise Dahara City takes up much of the film's second half. Long story short: Hoopa's giant form, which had wreaked havoc on the village 100 years earlier, is released from its bottle after Team Rocket tries to steal it and begins a new rampage on Dahara City with the help of six Legendary Pokémon it has summoned with its rings (Primal Groudon, Primal Kyogre, Dialga, Palkia, Giratina, and Kyurem), while Ash, Pikachu and little Hoopa summon some Legendary Pokémon of their own (Lugia, Latios, Latias, and Rayquaza). A decade later, Barza and Meray enter Dahara City, a modern Middle Eastern megalopolis patterned after Dubai (United Arab Emirates), and encounter our heroes, Ash Ketchum, Serena, Bonnie and Clemont and their various Pokémon. Hoopa, in his cute, dimunitive form, becomes the companion of two Arab children, Barza and Meray, who live in a traditional village, and pulls all sorts of pranks on the villagers. The giant form of Hoopa is indeed contained in a bottle like the one that housed the genie in THE THIEF OF BAGDAD and similar tales. Hoopa also has a giant form, with multiple arms and clawed hands, resembling a traditional Arabian Nights genie, as befitting the movie's Middle Eastern setting.
It offers at its center a mischievous little flying Pokémon named Hoopa, who talks and has a taste for donuts and boasts an extraordinary power found in the three rings it carries on its circular body in which it can teleport living beings and objects (some quite massive) from distant places to wherever it happens to be.
POKÉMON THE MOVIE: HOOPA AND THE CLASH OF AGES (2015) is the 18th Pokémon Movie and the second in the XY series (after last year's POKÉMON THE MOVIE XY: DIANCIE AND THE COCOON OF DESTRUCTION, also reviewed on this site).