I think potionomics is a great game to draw visual inspiration from for a 3D VN! Since a good chunk of a VN tends to be dialogue I think these sort of scenes work really well where you have a background, characters and then the text in the foreground. I would only say that it would probably be nice to break things up with the occasional cutscene when something exciting is happening. It seems sort of like a waste of 3D's inherent strengths if you don't do any fully cinematic scenes where you take advantage of dynamic camera angles, lighting, etc. This would be akin to how classic 2D VNs will occasionally have full illustrations for important scenes. Course I dunno if that would ruin your plans of doing everything in Blender :C
Anyway I wish you all the luck with development, this looks fantastic so far :D