I'd be fine with exhibit-style aquaria, but it becomes complicated when you start wanting fish that live in large schools. Cichlids are a good example of this, because typically in a tank the size of the in-game exhibits you'd need 50+ of them to create a functional ecosystem, and I'm not sure if anyone has the patience to sit there and adopt hundreds of tiny fish from the market to fill a tank (and that doesn't even take into consideration how often they would breed in such huge numbers).
For me I think there'd need to be some kind of compromise around creative freedoms. Big fish, such as moray eels which can live in a tank alone or in groups of 2-3, or even piranha which could happily be in a school of 6-8 in a tank the size of the exhibits, could be on the market, but it might be worth adding in 'scenic' tanks as well, i.e. pre-fabricated aquaria where adding animals is just ticking a box and letting the game generate the looped animation based on whatever box you clicked (so, if you ticked 'African cichlids' the game would generate an environment based on that choice, including a bunch of fish which swim around on a loop, saving you the hassle of having to refresh the market countless times).
In other cases, making fish into a special effect would be good. For something like koi fish, a little effect that you can place in a pond to simulate there being fish inside would be fine by me. 'Small' would be two fish swimming around each other, 'Medium' would be four, and 'Large' would be six. These would of course not require any management or care, and would solely be decorative, but it would serve the purpose.
I don't think we necessarily need the ability to build big custom tanks, though. They might one day make a game called Planet Aquarium or something where you can build a replica of, say, the Georgia Aquarium, with huge custom tanks for things like whale sharks and manta ray, but zoos typically deal with aquaria on a smaller, more manageable scale (some zoos do combine a full aquarium into their infrastructure, but this isn't common).