Also have to wonder if they had concerns about keeping it a zero cost trait would just incentivize people that went down biological ascension to throw the trait on all their pops if they happen to have a means to turn all their worlds into Gaia, relic, ringworld, ecumenpoli or ocean worlds. Mind you I'm checking the wiki and assuming it's correct and that I'm properly interpreting the information to mean that you either get the trait upon empire creation or mod into it. Didn't think to see if I could mod it in without biological ascension on my psionic fish pops (got zroni, so had to go psionic). If you can mod it in without biological ascension, well that makes things worse in a way.
if you nothing but the worlds I've already mentioned and it was still zero cost. There would be zero reason to not stick it on all your pops. In fact, that would make it one of the only zero cost traits you could add with gene modding and it's kind of easy to realize why that is likely going to always be bad design. More often than not, you get a scenario where it just becomes impossible to justify not adding it. At a single trait point cost, there is now an opportunity cost and that kills the incentive to add it to all your pops.
I also have to imagine that in additional to this being one of the best traits, the devs probably weren't crazy about the idea of aquatic making world shaper even less likely to be picked up (yes, Gaia world boost all production that isn't pop assembly, pop growth added by jobs, stability, amenities and trade value, but there are so many better ascension perk options than world shaper). Anyone can terraform a world into an ocean world and I'd argue that aquatic trait puts hydrocentric ahead of world shaper anyways; especially, if someone decides to go tall (god, I'm hoping sprawl and unity rework actually gives tall some solid advantages that wide doesn't have, while raining in the snowball ability of going wide).