I am looking to book on the humble Xmas time because of a special. anyone have an insight on if this is a bad idea? I know there is an el nino and its no peak whale shark season but is really that such a concern? thank you!
I've done 5 Galapagos liveaboards. 3 around Christmas/New Years and 2 in whale shark season (Aug/Sep). Two of the Xmas trips were on the Humboldt Explorer. Of the 3 Xmas trips, one had multiple whaleshark sightings (possibly same animal seen 3 or 4 times) - just damn lucky. One had the best visibility of any of the trips I have done, allowing you to see all the hammerhead layers behind the first layer of hammerheads you normally see

. The third was 'average' for the Galapagos, which means absolutely awesome diving.
In the summer I saw more whale sharks (luck permitting - I did one peak season trip where there were only glimpses of 3 seen) but visibility is also typically not as good. I have not had great manta experiences in the Galapagos compared to e.g. Indonesia but I consider the schooling fish, Galapagos sharks, silkies, black tips, sea lions, fur seals, dolphins, porpoises, turtles, etc. equally fantastic in summer or Dec. I have not done itineraries with the mola mola dive (Punta Vicente Roca) or swimming iguana dive so I can't speak to them. I liked the HE itinerary I dove because it maximized dives at Darwin and Wolf. Another factor in me choosing HE was that they were working with one of the most experienced and IMO terrific Galapagos dive masters/cruise directors. In my opinion the DMs are more important than the boat in choosing Galapagos liveaboards.
None of these trips have been in an El Nino. Were I in your shoes, I would be hoping someone like DiveTheGalapagos who has dove the Galapagos year round for several years would chime in about current El Nino conditions.
In my opinion you should not add days on the mainland. I have not done Machu Picchu (Peru), but many do - I would do that before Ecuador mainland. My #1 recommendation would be to hoard all the days you can for the Galapagos themselves. The land visits of dive liveaboards are somewhat paltry - nowhere near enough to experience the full magnificence and beauty of the place. I think you will visit Bartolome on the HE (and Santa Cruz, the most touristy of the islands) but I would seriously consider North Seymour and possibly also South Plazas day trips. I have done both multiple times and would do both again.
Or, depending on how much time you have, last time I was there I saw an enormous jump in the percent of liveaboard divers spending a few days in Isabela pre/post trip, which has a lot of wildlife and tour opportunities (including penguins) as well as a volcano hike, a very beautiful lava bridge area, etc.
All 5 trips I have done significant extensions, including land-based diving from Santa Cruz, San Cristobal and Isabela; day trips to other islands by boat; land-based Isabela, Santa Cruz and San Cristobal extensions; local exploring via foot, taxi or motorbike (very difficult to arrange motorbike - may be impossible now). All of these activities I personally enjoyed more than the time I have spent in Guayaquil (usually) or Quito. Due to a mandatory overnight on both ends, most people end up with some time in these cities in any case - I have often had most of a day on the way home to explore local areas.
If budget is a consideration, Santa Cruz and San Cristobal offer local beaches and hikes that I have spent many, many hours enjoying. There is a huge range of accommodation options in Santa Cruz/Puerto Ayora.
If you book, I hope you have a wonderful trip. Let me know how it went when you get back!