I think what makes the manatee controversial is that it keeps coming up as sort of a special treatment animal seperate from other aquatics, not that people dont want it.
It gets the special treatment because it's one of the very few full on aquatic mammal species that is not overly controversial in media.
We've known for a long while now that you don't technically need a full on new habitat system nor really have to completely overhaul the habitat system to allow full on aquatic species, the technical hurdles are certainly much much smaller than having full blown free flying aviaries; but when it comes to orcas, dolphins, etc. keeping them in captivity regardless of what side you are on is controversial.
Let this for the love of all things good and pure not be a starting point for a whole discussion on the ethics around keeping cetaceans in captivity, but we just have to acknowledge that the topic is controversial and
even if it's just a game, it just is a PR nightmare when it comes to socials. Nobody wants to deal with endless streams of fighting between the two very vocal groups on YouTube videos, Facebook/Instagram/Twitter posts etc. So that might be the biggest reason why Frontier has not added such animals in the game.
Which loops us back to the manatee. It's possible from a technical standpoint (we've gotten bigger reworks to existing mechanics before) and it's for some reason the least controversial fully aquatic mammal species out there, so that's why it's considered one of these ofshoot animals.
Do I think Frontier will add them? Most likely not. But I do understand that it is different from other animals like cetaceans.