Aegis works well, it provides ALOT of power toward your Aux and Weapons systems, if you want to whack people quick, Aegis is the way to go in PvE. Never worked too well in PvP for me, but Im a cruiser driver and PvP isnt exactly our strong suit anyway.
MACO does much the same power boost wise but to your shields and to your weapons. Its what you want your support ships in Elite STFs to be using, either MACO or Borg. MACO's set bonus, the kinetic death ray (I have no idea what its actually called) is pretty good if your opponent's weakened to about 10%, and your kinetic weapons are cooling down. Shields don't seem to stop it either. It deals direct hull damage, just get fairly close.
Actually, you've got the power benefits a bit off. Aegis is built entirely for defense, boosting your Defense (dodge chance) and Shield capabilities. The M.A.C.O. set is also a defensively oriented set, but it improves your structural integrity as well, and as an offensive benefit gives you a chance at boosting your power levels with every hit you take and recharges your skills faster.
The Omega set has only moderate defensive capabilities, but the 2-piece strips shields off of enemies and the deflector improves your accuracy.