Looking at footage of Tree Of Savior on youtube that game is 100% 3D. Flat shaded though. Basically texture is fed to an emission only shader.
No Sprite3D's or anything like that in it. Just low poly 3D models modeled and textured in a specific style. And animated at a low frame rate. These models are so simple I dare say it might actually be easier to develop your game similarly rather than going the Sprite3D route.
Or if you really want to create a 2D game just create a 2D game.