I prefer NOVA, only because gaming on iOS to me is casual. Modern Combat, is more hardcore/realistic. Where NOVA is more over the top, "fantasy/sci-fi" like. I'd rather jump into a quick NOVA game then a Modern Combat game. If I want to get serious, that's where a console or pc comes in for me.
So in summary, it's more fun for me to use crazy "Halo-Like", futuristic weapons and jump around a bajillion feet in the air, all while blowing away everyone in my way.
That's just my take on it.