Egregoria used to be 2D but it felt a bit restrictive. A lot of the underlying simulation is also 2D as I didn't port everything when doing the migration.
From the player perspective, 3D is the norm these days. It looks better, it's usually more intuitive and 2D is usually a bunch of tricks to fake 3D anyway.
From a developer perspective, 3D fits my brain better as I can translate real concepts better. To me, it feels easier modelling in blender and apply physically based rendering rather than learning lots of 2D techniques to have a consistent good looking art style.