I am new to the furum and hope the following suggestions help.
Take the advice about the currents they can be very strong sometimes, the "whale shark season" begins around May and ends around November, but it can move up or down a little bit, even within the peak of the season you get a bad week with few whale sharks and sometimes NO galapagos sharks or hammerheads, it is just luck sometimes.
I had to live through those bad weeks every now and then with the passengers complaining a lot, and even if you searched and searched there were no sharks around.
I worked as a dive-guide for the last 5 years mainly onboard the Aggressor and other boats, and dived the Northern islands year round, if you want to see a whale shark pick the season where you have the best chances.
From December until April-May the water gets warmer and you see just Galapagos and hammerhead sharks, you can also have a bad week with no sharks in this season. It is basically unpredictable when it might change and you get a week with no sharks at all.
The best diving is in Darwin and Wolf, if you can make it to these Islands, try.
Regarding the boats with permits, yes only a few are authorized now, and it will get worst, everytime you read an article about how tourists "destroy paradise" a bureocrat also reads it and some environmental NOGs that need some Projects to present to the Board too, so another "study" gets done and more restrictions arrive, some are good common sense and help to protect the islands, some are just "rubbish" I would prefer to use another word but I do not know if I am allowed in this forum...but remember that some people makes a living from "extinction" not conservation. To get funds you need to use the words that get attention and "extinction", "endangered", "in peril", etc. work very well.
The reason why DAN does not covers insurance on the Galapagos has to do with different viewpoints with the company that operates the private decompression chamber in Santa Cruz, not due to political issues with the government.
Take a signalling strobe in every dive (just take it don't turn it on while diving), a small flashlight in the day dives (just in case you get lost), a "sausage" signaling device you can display while doing your safety stop (it helps the dinghy drivers to locate you as you drift in the middle of the ocean), a mirror, a dive alert, a flag (some boats provide one some do not) if you are not in shape get in shape, (sprinting uphill is similar to swiming like mad after a whale shark, and you will need it, so start sprinting uphill).
Follow the guides instructions usually they are the first to find a whale shark. Ask the boat operator NEVER to anchor while they have divers in the water at Darwin or Wolf, so in case you end up drifting to Tahiti (a long way) they can begin to search for you inmediatly not after the 10-20 minutes it takes to raise the anchor. I am not trying to scare you but people have got lost and never found, even very very experienced divers (most of the time tour leaders or video crazy divers) that dived the Islands a lot got lost for some time before being found....it doesn't feels good.
Hope the advice helps, and enjoy your dives, it can be the best diving of your lifetime if you it the right week.