All Animation Is Disney: The film is often called a Studio Ghibli film despite not being actually made by them, but rather by Studio Ponoc with help from Studio Khara. This is understandable, however, given that Ponoc is formed by ex-Ghibli alumni while Khara has had a lot of involvement with Ghibli in the past.
It's the Same, Now It Sucks!: One common criticism of the film is that it's fairly by-the-book, following the beats of a stereotypical Studio Ghibli film with little to no deviation from the expected norm.
Moral Event Horizon: Madam and Doctor Dee putting Peter through the fly-by-night experiment even though the first time was a huge failure and it could easily cost him his life.
So Okay, It's Average: Critical and audience consensus seems to be that it's a good effort and a solid first movie for Studio Ponoc but not quite up to the standards expected from Ghibli alumni. Aspects like the script and characters needed a bit more polish, but the art and animation are beautiful and better writing will probably come in time once the Ponoc staff have had a chance to get some more experience.
Toy Ship: Mary and Peter have several sweet moments together in the film.