Atlantis, a shallow (pun not intended) attempt at faction diversity. Of could have just been given a t3 carrier like everyone else but instead they got a t4 just to be different. But then it would be too different, so instead they got a t3.5
That roughly sums up the whole problem, the Atlantis doesn't know what it wants to be, a t3 aircraft carrier or a t4 submarine, so it tries and fails to be both at once.
It's not a good carrier because its mass cost per BP is over twice as much as other carriers, in fact it's literally cheaper to build a t3 air HQ from scratch if you want t3 air units.
It's not a good submarine because its massive size, slow speed and relatively low hp make it a pitifully easy target to destroy.
The only thing going for it are its relatively cheep cost for a t4 unit, and its decently powerful weapons.
Essentially it is a glass cannon, a quick to build but short term boost to firepower. A gimped monkey lord.
There are a few options on how to rectify this:
Take a heavier focus on the submarine aspect, make it a little smaller, boost its speed, add some anti torpedoes. Make it threatening to enemies naval units.
Take a heavier focus on its carrier aspect, give it much more build power, more powerful AA, maybe even Airstaging (if adding that to a submersible unit doesn't break everything).
Turn it into a dedicated support unit, a t4 cruiser wannabe, using its AA and torps to discourage incoming attacks to your navy while offering extensive sensor range and fighter support.