I, in another group of 15 (this time 10 women, 5 men), attended a second run of this tour the week after Jaya's. The two tour groups were in fact due to meet up for a joint dinner as we crossed over for one night only in Quito - but the stars didn't align due to the severe delay the first group suffered getting back from the Galapagos Islands.
Just to add on a few extra tips over and above those already mentioned that may be useful:
* Nobody in our group picked up a bug thankfully, unlike the first group, but half the group felt the altitude in Ecuador to an annoying level, one severely. Most of the affected turned to the local herbal pills that the tour manager recommended which took the edge off. I was taking the prescription-only Acetazolamide tablets I bought from Dr. Fox online that did the same thing. They are available on private prescription only, so your GP will charge for it if you prefer to get them that way - like most travel vaccinations are now chargeable for protection again diseases not endemic in the UK.
* Duffle bags. It seems that our group did the exact opposite of the first group. Just two people took them to the islands; the rest stripped out what they didn't want to take to the islands - so warm clothes, used clothes, and single use plastic and left those in the duffle bags at the Quito hotel, to pick up on the return. JY's paperwork just created stress on this point by suggesting folks do it the other way around. Most people felt much more comfortable taking their own case on its travels rather than decanting into the bag provided. It is not an issue as the cases are fully portered on their travels - and the tour manager portered them himself in the one hotel that didn't offer that service (the dreaded Miconia - more on that later).
* Cases/bags - be prepared that these must be kept unlocked for inter-island travel by boat as they WILL be opened and inspected prior to every sea leg. Hand baggage is inspected at the port for each leg. For internal flights, they can stay locked and be opened on demand if required as they are x-rayed prior to check-in then have green tags applied to the locks to show they have been checked. They are looking for single use plastics mentioned in my next point on the way in, and rocks and other unofficial souvenirs on the way out and in-between the islands by sea.
* Single use plastic - JY's docs got this completely wrong. They said that single use water bottles cannot be taken onto the islands. They can. What can't be taken onto the islands are: single use plastic cola and beer bottles that do not have return-for-cash schemes running on them; single use plastic straws (you get metal reusable ones on the islands in drinks where they are issued); Styrofoam cups and food containers; and single use plastic bags. So if you wrap your shoes or used clothes in old supermarket bags from years ago, they won't allow those on the islands - you need to take obviously reusable bags like those pack-a-bag types that zip up into a small square. There is a nice chunky fine of something like $694 for every infringement noted on the customs declaration card you fill in on the way to the islands. This is made extremely clear before departing Quito and so nobody got 'done' for this infringement. I am glad to report that we did not see a single piece of discarded plastic anywhere, land, sea or beach - save for a baby's bottle that a baby threw into the sea off a boat pier when they'd had enough milk before their mother could save it. :-)
* Liquids - the trip to the islands is a domestic flight and so liquid regulations do not apply. You can take whatever liquids you want in hand baggage - subject to the plastic rules. You can also take liquids you bought post-security at either Heathrow out or Quito back through Bogota airport so long as you have the receipts showing that they were bought at the originating airport and not anywhere else. I had no trouble taking an open bottle of water and sealed bottle of Coke through Bogota where they checked the receipts. [I knew this from a previous trip through Bogota which is one of the most transfer-friendly airports in the world - unlike transiting through the US who make it as lengthy and painful as possible.]
* The Miconia Hotel. Good grief. Having done around 20 JY tours this hotel is without exception the worst I've ever stayed in, by the biggest possible margin. It's only one step up from a backpackers' lodge if the quality of my room was anything to go by. The bathroom was dirty with the previous contents of the toilet paper bin quite clear to see where the liner had not been changed; I felt the bathroom was electrically unsafe with exposed wires in the bathroom behind the world's oldest shower mixer, only topped on the horror's list by the cut into the shaver socket to run an improvised over-sink light with exposed wires to it as well. There were no usable plug sockets to recharge a phone/camera in the 'prison cell'. i.e. the bedroom which was just 3m x 5m connected to the smaller bathroom on one side and the outside door on the other side. I had to leave the blinds down at all times as anyone walking past could see straight into the room where I am only one metre away from the window. The air conditioner was old, situated near the top of the bed, and extremely noisy so could not be left on overnight as I can't sleep in a lot of noise. I traded noise for heat but still didn't get any sleep as a result. It never got the room below 80 degrees F and so the room was permanently hot and smelled damp. Even when my room's unit was off I heard the dripping from other units nearby whose condensation trap seals had failed. Perhaps JY thought they had booked the hotel's Seaside Inn rooms which would have matched the quality of the other hotels - assuming the pictures on their website are a true likeness, because they aren't for the rest of the rooms and facilities. This hotel needs to be replaced on all future itineraries.
While we were well warned of the step down in quality of the hotels on the islands compared to the mainland hotel (even then that was just a Holiday Inn Express instead of a full service Marriott over the road and Hilton around the corner) this hotel crossed a line and should not have been used. When I was 18 I would have put up with this level of accommodation - but not now I'm in my 40s and my comfort is raised - on a nearly £7,000 holiday before upgrades or optional excursions. Just three doors down the seafront was a 4 star hotel at four times the price that everybody would have preferred to stay at - and be willing to pay for on such an expensive holiday where the uplift would not be noticed in such a price - called the Golden Bay Galapagos Hotel & Spa. Most of us had a nice meal there on a non-include meal evening.
That one hotel aside the others were all acceptable to excellent - in particular the Albemarle on Isabella Island which was wonderfully appointed - and that is considered to be on the poorest island as well.
* TVs. Apart from the Holiday Inn Express in Quito which has CNN International, there were no English language channels at any of the other hotels. So no BBC World - despite the channel being listed in some hotels on the TV's channel guide. I guess they just didn't put it in their package. All other channels are in Spanish. Obviously the point of a holiday in not to watch TV, but it meant it was not possible to get any UK news while away unless you took a data-capable mobile phone or tablet - so trying to see whether Brexit happened or not by the time we got back on the 1st. ;-) Be prepared for the internet to be very slow from the islands. Basic e-mailing, web site reading and updating social media is fine - but you will not be able to stream audio reliably or video at all. Part of this is that the hotels run their whole Wi-Fi network off effectively a home broadband connection running a previous generation of technical connectivity than we are used to in the UK these days.
* A lot of people would have preferred it if the one day in Quito at the end was moved the beginning with the rest of the Quito days, as there is no logistical reason to put it there. Then, people could go straight home from the Galapagos, if necessary staying at a Quito Airport hotel for an overnight stay if flight itineraries dictate it - as it's a minimum one hour drive each way from/to the airport to/from the Quito hotel - and it just restarted the altitude sickness issues for the affected folks.
Doing this would also give JY the option to split the tour into a Galapagos tour with mainland add-on - so that those severely affected by altitude and so cannot pick this tour to get to the Galapagos, could avoid the high altitude bits and just do the sea level bits. Everybody went on the tour to see the Galapagos, not Ecuador's mainland - of which to be honest there wasn't all that much to see of great interest - so it would be minimum or no loss to miss that out. It also would encourage people to book the tour who still work and only have a week's worth of holiday days free, not two weeks' worth.
I think that's everything I can remember that others might find useful.