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Not having amulet of the fish isn't the end of the world. The aboleths and mind lords (and perhaps your pretender, if not naturally amphibious) are the only units that really benefit from them. The slave mages have almost the same paths as the aboleths, just less of them, but are naturally amphibious. So, you are not losing THAT much by using slaves instead of aboleths.

Magic leadership will be a problem if you are planning on taking your lobos or shamblers with you out of the water, but you can make a Crown of Command or two to help with that. However, out of the water you will be facing archers, and lobos don't hold up very well against archers. Use indy HI with shields as grunt troops as soon as you can get them.