This question makes me think about the games by Proton Studio Inc. I've enjoyed several of their games, including their 2 incremental games, Time Clickers and Time Warpers. They are both 3d games but with a fairly simple voxel aesthetic, and are fun to play actively/in the foreground, but provide mechanics to allow you to progress while idling.
In my opinion, the idling while still rendering all this 3d stuff feels awfully wasteful, but I do really enjoy the time I spent actively playing. And I think that's what it ultimately comes down to - 3d can definitely be used to build engaging mechanics that are really fun, but if you go that route I'd actively discourage implementing idle mechanics (the genre has enough examples showing that you don't need them, anyways!) or at least make it a separate mode where all the 3d stuff isn't consuming resources.