These being my two all-time best dive destinations...
The topside wildlife attractions in Galapagos are excellent...birds, seals, marine iguanas, etc. The diving at Wolf and Darwin was big animal action at its finest...a SINGLE dive produced 75 hammerheads, a huge squadron of eagle rays, and a 40+' whale shark.
Ecuador is really an interesting country, too...we spent two days exploring Quito and the surrounding areas. I liked the people immensely.
Cocos has a special sense of remoteness (not that Galapagos was a 'local' dive...). The island is primordial-looking with waterfalls and clouds of mist...being uninhabited (except for park rangers) adds something to the allure, too.
We were treated to witnessing a baitball feeding frenzy that was spectacular...seabirds dive bombing a giant school of green jacks from above, tuna, sharks, and dolphins ripping through it from below...it was a NatGeo moment for sure.
I don't know which I'd go to see first, but for a repeat visit I'd probably choose Cocos.