After having done some research recently on both boards, it all comes down to what you're wanting to do wit it long-term..
If you're wanting to upgrade later on; the H97-Plus is very versatile.
Seeing as though you're going for an i3 processor, I'd go for the H97M-E - mATX if I'm not mistaken?
...on another note, I'd stick to a MOBO and GPU of same branding. Seems like you're wanting high end graphics.. Why not go for an i5?