My idea for combining the vanilla and sequel maps was more just a side-thing than something for the sequel itself. If there's one thing I love, it's combining or otherwise compiling parts of different entries in a series together. For example, one of my projects is a map Hyrule and its neighboring kingdoms from the Legend of Zelda series that, while based primarily on Breath of the Wild and Adventure of Link, incorporates elements from plenty of the games. So combining Aquaria's original and sequel maps is more of a just for fun thing. It would be hard to make work plot-wise the way I envisioned (Aquaria Expanded as opposed to Aquaria 2) due to the time gap between the two games.
That said, I could see the original areas being implemented in a way akin to Pokemon Gold and Silver, where after beating the main game, you get to visit the first game's areas as a little bonus. I think it'd be nice if the first game's areas were all there, even if they don't serve a role in the story, but they're not necessary.
quick rundown: the 6 energy temple maps, 3 veil maps, mithalas + cathedral, top 2 open waters maps, the starting area things, Li's cave, one forest map
What forest map?
"Cold waters" sounds indeed interesting.
What about Warm Waters? Your open area is in the right place (near the Energy Temple, which if it weren't for being underwater would totally be the Fire Temple), and still doesn't have a name. Adding some "warm" elements would give the place more identity, but then again, if you're not gonna revisit old areas, and this is the new Open Waters, maybe that's not a good thing. Even then, though, a sequel shouldn't be a retread, so there's no harm in a slightly different atmosphere. The biggest issue would be figuring out what exactly the "warm" elements would be. The Veil and the area directly below it are already tropical, so you can't exactly do that. Maybe hydrothermal vents? As shown on my map, I was thinking of putting a volcano above Warm Waters as the logical extension of the "warm" aspect, and hydrothermal vents would tie in nicely to this. A warmer color palette would make sense. I tried doing a mockup with warmer colored rocks, but it just ended up as an ugly brown. Maybe changing the background gradient would be a better idea.