The problems with The Shape of Water have already been covered extensively by other disabled activists, so I won't delve too deeply into it, but one of the biggest issues with this movie is the idea that disabled people are unlovable and do not belong with other humans.
The protagonist, Elisa (Sally Hawkins), is a Deaf woman. Because she cannot communicate effectively with others (or more precisely, others cannot communicate with her because they refuse to learn to sign), she spends her life in isolation. She works as a janitor in a government laboratory, where she meets the sea creature who becomes her love interest. Elisa falls for this creature not only because they both share the experience of being different, but also because the creature does not notice her deafness.
While many people think it is progressive to not see (read: acknowledge) a person's disability, they are really just denying a part of that person's humanity. For the most part, people who claim to not notice disability are projecting their own discomfort with it on a disabled person.