Atlantis is a support unit used by UEF to counter submarines and also give brief airsupport. Its a multifunctional unit. The reason why its a support unit is because if you get it out at the front or in the open BSHIPS rape it. However, if it sits in the middle of your crap, it absolutely rapes enemy submarines.
Simply put UEF anti-subs are crap. Coopers are crap. Coopers are also very vulnerable to frigates.
Atlantis is not crap, it has decent DPS, nice HP, and is not vulnerable to getting bumrushed by frig spam. So you sit it below your bships somewhere near the center of your army and its very useful, so long as you have a good wall of frigs and shields to protect it.
For the cost of an Atlantis its actually more efficient than Seraphim t3 submarines. So don't knock it.