Galapagos and Indonesia are my two favourite dive locations in the world but they are so unlike each other to be almost incomparable. My background: 5 Galapagos liveaboards, land-based diving from Santa Cruz, San Cristobal and Isabela, 2 Raja liveaboards, 5 Komodo liveaboards (and myriad other Indo trips - see my profile).
For me the most breathtaking things about Galapagos diving are the intimate encounters with sharks, sea lions, dolphins and enormous schools of fish and the incredible wildness of Darwin and Wolf. Indonesia OTOH is about beautiful, colourful reefs and incredible biodiversity in fish, critters and corals, as well as really diverse underwater topography (full disclosure: I love Komodo and Lembeh but am still lukewarm on Raja despite two disparate 14 day liveaboards).
Galapagos highlights:
- intimate encounters with enormous schools of hammerheads, individual hammerheads, huge Galapagos sharks, blacktip sharks, silky sharks, porpoises, dolphins, massive whale sharks including pregnant females (whale sharks should not be "occasional" on liveaboard trips unless you go out of season, or with a weak operator, or are very unlucky). The quality of these encounters far exceeds my experience with e.g. Mozambique and Bunaken whale sharks, Caribbean and Hawaiian dolphins, schools of fish most other places in the world, etc.
- schools of rays (mustard rays, eagle rays); mantas
- sea lions and Galapagos fur seals (fur seals were a special trip)
- penguins (topside, floating, and even underwater if you are lucky)
- endemic Galapagos fish (and a few critters)
- large and mating turtles
- large tuna
- schooling juvenile Galapagos sharks and we saw orcas from pangas at Darwin (but not underwater, and the whale sharks vanished as a result)
- enormous schools of fish, including rivers of creoles
- This is not even including mola mola, feeding marine iguanas and Galapagos horn sharks which I have not seen personally yet.
- I have to also mention the incredible topside wildlife encounters, again, often very intimate (sea lions including juveniles, iguanas, tortoises, flightless cormorants, frigates, red and blue footed boobies including chicks, Darwin's finches, etc)
Indo highlights:
- gorgeous fishy reefs
- mind boggling diversity of corals, fish and critters, including rare critters and awesome cephalopods
- some large schools of fish (by large I mean 100 or larger)
- terrific diversity in underwater topography (muck, pinnacles, walls, bommies on sand, blue water mangroves, coral slopes, bubbling volcanic sites...)
- some sites you can have beautiful visibility
Major differences:
- Galapagos has much colder water. You can easily have high 50s *F in Isabela and San Cristobal (Darwin & Wolf are warmer)
- you are not looking for 'coral reefs' in the Galapagos. While there is coral, most of the diving is around life-encrusted boulders or walls, or there are some blue water drifts.
- Galapagos has lower vis generally than Raja, though in Northern hemisphere winter you can get better vis in Galapagos and I've also experienced some really low vis in Indo, including in Raja
- I actually prefer Indonesian manta encounters to Galapagos for the clearer water and longer encounters (e.g. Manta Alley and Magic Mountain)
- My experience is that the currents in Galapagos are far more manageable (and usually weaker) than those in Indonesia. I've seen more un-fightable down currents and side currents in Indonesia. That said, most of my Raja dives didn't have strong currents.
- Galapagos dive times are generally shorter both because of the conditions and the dive profiles (e.g. 3 different liveaboard companies all limited dives at Darwin and Wolf to 50 min). I had dives with land-based Galapagos ops that were even shorter.
As you point out, there is always the option to do Galapagos topside with land-based diving. Definitely you can dive with sea lions from land-based ops. I've had some wonderful sea lion interactions on SCUBA, but other dives where divers were ignored (some sites seem better than others for sea lion encounters). You might need a naturalist cruise if you're dead set on seeing marine iguanas feeding underwater. While they are pretty common topside, I'm not sure how easy it is catch them feeding. Definitely you can see groups of hammerheads doing land-based diving, just not as reliably, in as large numbers or as close as those in Darwin and Wolf. You can do some wonderful topside day trips with land-based ops.
Whether you will love Galapagos as much as or more than Raja I think really depends on what you love about diving.
Hope that helps.
