Unity is fake 2D (locked orthographic 3D), and while it works for plenty of people there are plenty of reports of the tools being very difficult to use.
Godot has always been first and foremost a 2D focused engine, with 3D available if you want it. It's also far smaller and completely free (MIT) so you can make any changes you want at any level.
I don't use Unity, because throwing around vertex buffers isn't particularly difficult, but this is a pretty silly comment. Quads in an orthographic projection is what's done by literally every modern engine that's designed for any level of performance. "Fake" 2D is normal 2D in 2017.
2D is a special case of 3D. If you only want to do 2D then a 2D API is going to be simpler than a 3D API. There's a whole mess of parameters and transformations that just go away.
Godot has always been first and foremost a 2D focused engine, with 3D available if you want it. It's also far smaller and completely free (MIT) so you can make any changes you want at any level.