I care alot about the Elf species. I am satisfied with the 2024 Players Handbook format. It works well enough for any and every Elf concept.
If the DM needs to do something new, write up a balanced cantrip or spell for it. Done. Even write up a feat for it at the appropriate levels (origin, level 4, or boon).
Except they’re not doing that, because there isn’t a ‘wings’ or ‘gills’ cantrip and it is never even vaguely insinuated they’re altering their bodies with magic,
The elves shapeshift magically.
According to the Players Handbook, they lost the ability to do it "at will". But they still shapeshift "subtly" "over a millennium", in response to an environment.
Not all cultural magic is spells. People also learn how to do nonspell magical effects. This can include a cantrip-like benefit.
The Elf cantrip-like effect, such as Darkvision 120, is explicitly one of the "certain kinds of magic".
they fly and breathe water respectively by having physical adaptations they are born with, expecting a species to constantly be casting a spell on themselves so they can settle in an environment they’re fundamentally not suited for is just plain stupid, an elf isn’t a sea elf if there’s a chance they can drown by accident because their water breathing magic ran out or a sky elf if their wings can run out at the wrong moment.
If using the 2024 Elf, the waterbreathing can be its cantrip-like benefit: magic, but not a spell.
(It could still be learned culturally, whether the parent did a "mythal" ritual, or the child learned how to work this magic. Or both.)