Simple answer?
CoSA works on Gotham and Agents of Shield. But they don't work on The Flash and Arrow. Read how much visual effects work goes into a single episode of Gotham.
Longer answer?
The people who work in Gotham's art department have worked on major films like The Avengers, Ant Man, Shutter Island, Catch Me if You Can,
Some of the people who work on the visual effects for the show have worked on movies like Guardians of the Galaxy and Mad Max: Fury Road.
In defense of Flash, they've got a fucking gorilla. They have to be very judicious with where they use their visual effects and that usually means prioritizing fight scenes over environments.
But yes, budget and location means Gotham has access to a better pool of talent. Although AoS is no mark of quality.