When you play a Merciless enemy, it is always wise to "dig in" your base and prevent yourself from being overrun. The best faction for defenses is definitely the Federation. I you choose the right avatar, you can get the Torpedo Turret, which is the best defense you can get. The Phaser Turret are good secondaries and the Pulse Turrets are the weakest you can get. When you build your defenses, be sure to establish a distant perimeter between your defensive lines and your main base. Also use Nebulae and Asteroid fields to your advantage, the AI hardly goes through nebulae and you cannot enter a dense asteroid field. But separating your defenses from your main base allows you greater response time aswell as decreasing the enemies chances of damaging key facilities.
*NOTE* Sensor platforms are invaluable against Klingon, Romulan and Breen ships. Be sure yo build one Sensor Platform for every 4-6 Defense Turrets.