In MA, I always Prophetize the starting Illithid Lord. He's 40 Regular and 40 Magic leadership, is physically strong, and I won't have to choose between Smite and all of the wonderful goodies that R'lyeh's mages can cast.
In EA, the choice isn't quite so simple if you want Magic Leadership on him very badly. Personally I would also Prophet the Prince, and just have an Aboleth travel with him to carry the Lobos/Thralls.
EA is fun, but by no means easy to play. If this is SP and you are intrigued by R'lyeh, you may want to start with MA, their advantages are significantly easier to exploit. Then once you have the hang of what it means to be an aquatic nation, then switch back to EA and learn what it means to be STUCK in the ocean, and have to really struggle to get out.

By all means, you can keep trying to learn EA first - I did a lot of that type of thing when I first started playing as well, but it can be painful and frustrating.
