I prefer the linked rear. Back when I decided I read a whole lot of articles discussing suspension theory, less than half of it made a whole lot of sense to me but what I did understand led me to keep my factory linked rear. Probably the best argument for linked rear suspension is that it is what's still used on the most modern swing arm quads still produced today.
Pro for non-linked rear is less weight and less complicated. Ktm runs some non-linked on their dirtbikes but I know it takes a very specialized shock and shock tuning to get it to work well.