Quick bug report: the "new" EA R'lyeh is still in MA, you forgot to switch #era 2 to #era 1
Beside that,great work! I'll be testing it in a couple of games in the next days, and I'll report anything I find.
Regarding underwater fortresses, while the common nature fort site almost made underwater fort building redundant, especially with high magic site settings, it actually gave a chance to land nations to secure a water foothold.
This is just an idea that springed to my mind right now, but perhaps you could consider letting all land nations build an underwater fort? Make it one of the very expensive ones; it won't give national units anyway, I think; but it still will be useful as a hiding place and as a resource/supply centre. After all if humans get to magically breathe underwater, what's stopping them from building an outpost while they're at it
