Setting this in the Nolan continuity is ridiculous, as it will mean it'll lack supervillains. I'd actually be interesting if it were set in a more colourful world.
It should be set in the Arrow universe. It seems that in there, supervillany is rising as a reaction to Ollie's actions rather than the other way around.
Putting Gotham PD into the Arrowverse could serve as a means to see how supervillany is rising in the Arrowverse as well as be a launching pad to introduce more superheroes and establish a new linked television universe similar to the DCAU.