While I had a pair of 2nd-gen EE brakes, I didn't try them with Dura-Ace 9000. From what I'm aware of, the pull ratio of the latest Dura-Ace mainly differs for the shifting and the braking is improved because of the calipers and not brake cable pull. A friend who showed me the BR-9000 caliper for the first time last year nearly crushed my thumb with it. Its power improvement is definitely in the brake geometry. In contrast, EE brake modulation is dead linear and more sensitive to lever pull.
EE brakes were redesigned from the originals to be better compatible with wider rims as well as Dura-Ace 7900 levers. Since 7900 and 9000 calipers are interchangeable, any EE brakes 2nd-gen or later will also work fine with the newest Dura-Ace.