I've been using Unity3D for a while now and I've also had experience coding 2D games using LibGdx.
In the past, I used to get my sprites off the net or make my own however that wasn't really the best way to do things since I'm more of a programmer and would sometimes need very specific things and so I've started to learn blender and I'm actually enjoying it atm.
What I want to know is how much of an overhead is it if you're using 3D models for a 2D game? Especially if you want to port it to mobile?
The overhead is significant for rendering since with a basic sprite, you have 6 vertices (2 tris to make a quad) while a 3d model can have hundreds of thousands of vertices.
The advantage on the other hand is that animations are made of sprites, so your texture amount and size may increase. In 3D, an animation is a text file so fairly light.
The physics is simplified in 2D since you can do surface collision while 3D requires volume collision and obviously checking an extra dimension is more expensive.
There are probably other considerations but those are the first coming in mind.
Now, the choice of 3D over 2D should be simply based on what you are trying to achieve. Side scrolling games like Angry Birds do not need 3D. Games like Taichi Panda are better with 3D despite being a 2D game (only x and z camera movement I think).
A FPS game should only be done in 3D or it will look like Duke Nukem.