I own the iPad mini 4 and the 12.9 iPad pro. I like them both, and it would be tough to choose between them.
I'm a teacher and use the iPad 12.9 for work as a virtual whiteboard. Because of that, it's the one I'd keep if I were forced to choose one or the other. I also use it as a math notebook, and it's nice for watching movies.
But I do also love my mini 4 for it's portability. It goes everywhere with me, for reading books, checking e-mail or the Internet, taking quick notes, and as a GPS device.