Hi all.
I have some experience now with eTTL underwater. As a Canon shooter who bravely/stupidly dives with his 10D in a EWA-Marine housing, I do at least have the advantage of using my 420EX in eTTL mode. (My setup got it's first real use underwater a couple of weeks ago during a week at Ningaloo Reef, and I've just been assessign the results in the past few days.)
Shooting with this combo, I found that eTTL worked well underwater, but flash and general exposure compensation were both very helpful/vital.
The best mode generally to shoot in was Av, which on Canon SLRs/DSLRs exposes the background for ambient light, and uses ETTL to correctly expose the foreground. You can thus adjust foreground/subject exposure with flash exposure compensation, and background exposure with general exposure compensation, to get the balance you desire.
Manual mode works bst for macro, as you can control and use large depth of field (shutter speed in Av would be too slow).
So the eTTL definetly works, but I'd always want the ability to tweak my exposure settings as above. It's vital above water. and I think even more so underwater.
If 300D+Aquatica had a mode of flash exposure compensation, it would be great. If there's no means of flash exposure compensation, eTTL functionality would be cripppled (in either Av or M, your shutter speed and aperture don't affect the foreground subject flash exposure - ie., you're completely relying on the automatic flash exposure which like all automatic exposure systems will sometimes be wrong).
Despite the above comments, I'm very excited about Aquatica's development. Good work, chaps!