Atlantic Accellerator was easy to beat - once you knew how and weren't afraid to use this method. Firstly, it's damned hard to do with an unexpanded system because of the low framerate.
Once you've overcome the real world hurdle, here's how you beat it.
Send in four heavily armored agents with nothing but medkits. That's right, nothing but medkits.
Patiently wait for the bad guys to mob you - let 'em get close.
Then blow up your agents. That's right, self destruct them. By this point in the game you should be able to produce agents that can juuuuuust survive their own self-destruct mechanism. However the bomb is powerful enough to kill enemy agents that are too close, which is what you've gotta do. Get up close, then kill your agent.
Once done, start with the medpacks immediately.
Then grab all of the guns dropped by the enemy agents and go to town on the remainder of the bad guys!