Yeah, I can see where you're coming from on paper Micah, but I'm basing my position on the games I've done well with Atlantis (again, MA), and I just don't see the massive late game power gap you're describing in practice. Part of it is probably lightless lanterns, part of it is (assuming you've made it that far) controlling the water you have a lot more freedom to castle up, invest in research items/mages, not build troops, not forge combat gear, not loose combat mages etc. durring the mid game boom than you do in the wide open melee on land. Even moving fairly briskly to get onto land you can clobber the hell out of somebody already in a tight war without using too many resources. I don't know, I suppose my argument isn't terribly compelling based on foggy recollection from a sample set of two games.
My experience actually playing them in MP is early game requires some fancy footwork against the underwater opposition, sneak attack onto land is *easy* gains which can likely be repeated a second time if it's a big game, pulling into late game you've got a lot of raiding mobility, powerful battle evocations and powerful alterations from recruit anywhere mages and a good income (voice of tiamat) on a easier than average to defend kingdom. Granted EA Atlantis does seem a bit weaker on that front, Mages of the Deep are vastly inferior to Kings of the Deep and about the same price so you probably have a point there. EA Atlantis does seem to suffer from having nothing at all exciting to recruit from non-cap forts, a cheap research mage might work well there. MA though I think is fine.