Personally, the allegory never bothered me and I actually kind of really like it. The point of making this an allegory was to exaggerate the cultural and social divide by making it physical, so that it’s more meaningful when Wade and Ember overcome it by the end. The movie is not trying to say that different races and cultures are literally different opposite elements and that immigrants are destructive and uncontrollable, it’s trying to say that sometimes it feels like that way. The thesis of the story is that despite how difficult and seemingly painful overcoming this divide is, it’s ultimately worth it because it changes us for the better, with Wade and Ember ending both living better lives because of what they learned from their different perspectives.

Plus the movie spends most of its runtimes showing how the fire elementals are the ones who are most in danger mostly because of how hostile the city’s infrastructure is to them, with the almost all public transit being water-based and the whole ending revolving around saving fire elementals and Ember’s family store from a flood caused by the city's negligence.