I actually really like the heavy keyframed look of Flying Phantom Ship, which really makes the filmmakers focus on the composition of the frames vs. trying to dazzle with the motion. You can see the quality of the drawings, backgrounds, but it's clear they are fighting above their budget so to speak.
The first half of this film, before we get to the revelation about the undersea element, is such a wild ride. Honestly, this movie has as much going on as entire seasons of TV shows. The idea of this menacing Phantom Ship is very evocative. When a giant mech ostensibly from that old-timey Phantom Ship attacks the city, I was there for it. Even when the story is reframed as a anti-capital narrative surrounding a secret cabal of private and government interests all working in conjunction to enrich one another, I thought it was fantastic.
Unfortunately, as you might have guessed from that description, this movie just keeps trying to top itself over and over. Moments after that last revelation, it turns out there is some incredibly vague other threat that was controlling that other threat, and it keeps chasing its own tail down that endless rabbit hole. That the actual images are so well done, the mechanical drawings (of say the tank and the Zissou-esque cutouts of the inner workings of the FPS) are marvelous. What this movie lacks in execution it somewhat makes up for in ambition, but less would be more - much, much more.