I just discovered this really awesome thread, I have a few of my own that came to mind after reading through:
Monterey Bay Aquarium's "Into the Deep" | The largest Deep-Sea Exhibit in North America, this exhibit went through some drastic changes between concept art and final product (most of them I would say for the better though). I've gotten two BTS looks at the exhibit and know some aquarists from it so I can provide some more insight on why some decisions were made.
(Sorry most of these photos are terrible, most of them I pulled from the web since every time I visit, I always photograph the animals instead of the whole gallery)
ROV Statue: Right next to the basement floor viewing for the "Open Sea" tank, there were plans for a large ROV replica statue that guests could stand next to for a photo OP. Along with some signs explaining what an ROV is and it's uses.
Instead, this was scrapped and the result was an area that has a diorama of the Monterey Coast and Monterey Submarine Canyon where most of the animals are from, and a wall highlighting MBARI's work and some prominent scientists that are apart of MBARI.
"Science at Sea" | This area was supposed to be modeled after the inside of a research vessel, with various video screens and an ROV type game where visitors could play as an ROV piolet, maneuvering through the water and collecting animals.
Instead, this was scrapped and instead we got the 4 player "Midwater Survival Game" where you select a small predator to play as, and pick off different bits of marine snow. The catch is some of the marine snow are actually microplastics, and at the end, it gives you a summary of how much food to microplastic ratio you ate and why this is bad and more conservation facts. Which IMO was the better move for a public education stand point since it's very alluring to people of all ages.
You can also see a Sea Pig Tank in the room, which unfortunately the species hasn't made a debut yet because the Aquarium hasn't figured out what they actually eat yet (there was some testing going on at MBARI's facility to keep them alive for the exhibit, they tried blending various foods together to mimic marine snow, but it didn't work out). One day we'll see Sea Pigs kept successfully hopefully.
Midwater Room | This actually turned out pretty similar to the concept art, the only difference is that the circular inwall tank on the left is more of an oval.
The main thing is the big cylinder tank in the middle, while it is that way in person, the system unfortunately isn't designed to house Siphonophores in it like the concept art shows. The main reason is because the system the Aquarium uses on a smaller tank on exhibit called the "Tube in a Tube" system, wasn't able to be replicated on a larger scale (yet), so it's only displayed a few species of Comb Jellies so far. Which means no medium sized Siphonophores for the time being
Smaller Spider Crab Tank | The concept art for this shows a smaller tank for juvenile Japanese Spider Crabs, however this tank never made the final cut. I'm not sure why, but I'm guessing it's because the Aquarium's Spider Crabs are already so massive (last I heard, 2 of them are 10ft across, 1 is 8 & half feet across, and 1 is reaching 7ft across), there's not much more room to introduce more Spider Crabs to the group so having a grow out tank would be kind of a waste of space.
Instead, sometimes other Deep-Sea crabs are displayed in the "Muddy Plains" gallery time to time such as the Porcupine Crab.
Hydrothermal Vent diorama | I remember seeing an old rendering for the Hydrothermal Vent diorama where it would've been similar to the existing Bioluminescent room where you could walk in and be surrounded by screens playing videos of the underwater volcanoes and animals, and lots of figurines of the animals that live there. I can't find that picture anymore, but in reality, it's 1 screen with 1 viewing that you can look into with dioramas of the Worms, Fish, and Crabs that live there.
IMO most of these changes were for the better, especially the Midwater game instead of an ROV game. Honestly most of these are just animals that haven't been displayed yet that were featured on the concept art, which we could see in the future because the Aquarium has already cracked the code to so many animals so far, I'd imagine they're not far away from getting some of these other species on display (besides the ones that have size constraints).