As it stands, I believe the Atlantis is a very underpowered unit. It's health is too low for it to last long, while it's torpedoes I find to very little damage in the short time it lives, even with it's longer range. The SAM launchers on it's back are a nice touch, however I find they get little use in practice since most players will only have air engage navy if they have navy engage navy, where the Atlantis will either stay submerged or hang around at the back. The Atlantis has excellent range for it's torpedoes, but it's not like it can kite like destroyers and battlecruisers, meaning a bunch of sub hunters or torp bombers can sneak up and kill it. The ability to construct air 3X fast as an air factory sounds nice, until you realize that 3 T3 air factories are way cheaper and can take advantage of adjacency. It isn't like the Fatboy where you may be at a forward position and need engineers to reclaim or something, because Naval forces need to be constantly mobile, and air doesn't take long to get to the front.
The lack of default regeneration limits the longevity of the Atlantis, . It won't be getting many kills to boost it's health either. In addition to this, even while submerged, groundfire from other naval units and alot of land and air, will still do full damage. Because of this, it can easily die even to units it theoretically counters, like opposing battleships. It does have a range advantage, but that does not allow it to escape damage from opposing navies because of groundfire. Lets take a brief look at the other "Naval experimental."
The Tempest, which costs twice as much as the Atlantis, can take on 2 of them at the same time with just it's torpedoes and walk away with a good amount of health and maybe a veterancy to boot. However, if you take the time to babysit your tempest, you can groundfire Atlantis on it's approach from far away, and it's torpedo defense can negate a lot of damage. Because of this, a well microed tempest can take on THREE Atlantis and win easily. Heck you can even throw in a bulwark or two, it won't make a difference. The Megalith can come in and force Atlantis back, without taking much punishment. Strategic bombers, trebuchets, battleships, soul rippers, anything using groundfire with decent AOE. Even the humble Klink Hammer can lay down the hurt on a submerged Atlantis. I've tried using the Atlantis, and it's really frustrating when I find that it can't do any of it's roles well, not against decent players. Really, I find little reason to ever build an Atlantis at all, except perhaps in rare cases on huge maps when I already have a navy advantage.
In my opinion the Atlantis should be buffed, or at the very least they should decrease the groundfire damage when under water (and if that's already done, then do it a bit more).