What would be more natural for Aqua-Mage than weaving together polished bits of bone, tusks, stone, shell and coral with byssal & baleen to permanently capture magical writings? Scrimshaw also springs to mind.
I devised a spellbook in a similar vein, a dreamcatcher filled with spell tokens (Complete Arcane). As for scrimshaw, I had a pirate bone creature of the same name.
Like other people have said, there isn't much support for the rules, and the environment tends to limit player's options. If there was an actual setting to work with, I think these problems could be taken care of.
I agree that, for those looking for official rules, options can be somewhat limited; Stormwrack, Into the Blue, and The Deep seem to be the most thorough treatments, thus far, and of course all are out of print.
As for the environment being limiting, I tend to think quite the opposite. There are undersea analogs of most Drylander environments; forests of kelp or mangrove roots, a jungle of floating sargassum seaweed, “deserts” of bleached corals or urchin barrens, fields of seagrass, and brambles of living sea stars come to mind, as well as the more extreme settings of black smokers (hydrothermal vents), cold seeps (undersea lakes), and the blackness of the abyssal depths themselves. Add to this the dangers of a three dimensional world; Drylanders sailing upon the surface of the sea, shallow-dwelling and amphibious creatures lurking just below them, beasts which roam the open seas, and the mysterious bioluminescent world of the deep.
Did anyone like 3.x Stormwrack?
Absolutely! Stormwrack was very inspirational, to my current game. Blackwater, riverine, and pearlsteel found instant uses, as did many of the monsters mentioned within.
I've always wanted to use the underwater race(s) from The Abyss for a D&D game... what would their race and civilization look like during their medieval period?
In my last game, I had “abyssal elves”, inspired by the same movie. They were taken from drow stock and became a race gifted with “hydrokinesis”. I also have my ephyra, a psionic “mer-jellyfish” race.
...if you're playing a mostly above-water campaign and you suddenly go into the ocean ... what exactly do your PCs wear and utilize?
That’s one reason that I set the following stipulations for PCs in my game; they must have a natural swim speed and the ability to breathe underwater without the use of magic. Savage Species also has a “Ritual of Gills” that grants the aquatic subtype, if you are looking for something unconventional.
I've always wanted to develop a 1-20 full campaign set in my Japan inspired horror setting, and at higher levels, I wanted to include an undersea adventure.
Very nice.

In my current game one PC is a sea elf ninja, while another is a merfolk shugenja.