I say Nick Fury, 6/10 of the time. Mainly due to experience, and due to the fact that it seems like Mystique tends to rely heavily on shapeshifting.
I don't know about him having more experience than Raven. IIRC she is VERY old (80+ years I believe). I think Fury is a better fighter over all and has more impressive showings skill wise, but Raven's shape-shifting and enhanced physicality definitely gives her an advantage in surprise attacks (especially since she too tends to have a gun and blade with her), and an edge in close quaters. I'm not sure who wins here yet, but I don't think Fury has an experience edge over Mystique and her shape-shifting can be a big boon here.