My wife and I returned from the Galapagos in late Sept. Had a fabulous time on a 10-day trip on Sky Dancer. Originally, chose Sept. because it is supposed to be prime whale shark season. The downside is the water is colder at this time of year, and the seas are rougher. We saw all the usual suspects: eels, rays, mantas, red-lipped batfish, dolphins, penguins, sea lions, and melonhead whales. Biggest highlights were two whale sharks and tons of schooling hammerheads. Absolutely best diving we've ever seen.
I've never been to Cocos, but have done similar research to you and also spoke to divers who had been to both. So with that caveat, here are my pros and cons for the Galapagos:
PROS: Fabulous diving with the opportunity to see whale sharks and hammerheads. Relatively easy to get to (you fly directly to the islands in order to catch your liveaboard). Shore excursions are fascinating and a great way to spend your surface intervals.
CONS: One of the most expensive dive trips around, though perhaps not much more expensive than Cocos. Water is fairly cold (usually 60s during the prime months of July to November). Don't recall what the water temp is in the Cocos.
From what I've heard, the general consensus is that Cocos has more shark activity. However, one diver on this trip told us that he thought the activity on the Galapagos was better. Luck of the draw, I guess. The only other comment I've heard is that the 36 hr. trip to Cocos can be brutal if the seas are rough. That in itself is enough to sway many people (me included). Have fun wherever you end up!
