I do like the federation B - much better than the A.
For those talking about the Stealth Ship... honestly, I think it's probably my favorite. If you're going to lose with it, you usually know quickly enough to restart, and if you make it through to sector 3, the rest of the game is your oyster.
Both versions start with awesome weaponry, and I don't think any other ship in the game even comes close to matching it's initial damage output. 6 damage every 11 seconds is nothing to look down on. Properly timed cloaks give you enough time to pull it off. (I've actually found it's better NOT to put more than one bar in the cloak for the boss - I'm pretty sure his power surge countdown timers keep going even if you are stealthed, and one bar means you can cloak more often than with three. I may be wrong)
I do recommend getting shield ASAP - a single level is usually enough to deal with enemy beams and the occassional laser you can't dodge. Don't be afraid to sell your shitty but valuable titanium. After that, there's a couple of pieces of equipment to be on the looking for:
5-shot burst laser - Beams work best when there's no shield. For type B, this has about the same charge time as your glaive beam, and pretty much guarantees it will do damage. These two weapons together can do 17 damage in a volley on an enemy with no shields, which is why you want... And even with the A-layout, of course, the 2 damage from the Dual laser, plus the 5 from this, plus the 4 from mini-laser is still an impressive 11 damage.
Ion Bomb - Deals a large amount of ion damage, for a long time, for very little power. Guaranteed to knock down two points of shield. Launch one of these before your 5-shot laser -> Beam attack, and the enemy will be on his last leg, if not dead. Best part? It, alone, guarantees success for all but the 5-shield enemies, who are extremely uncommon.
Defense Drone - MKII is better for you, unlike most ships, since you have low shield, but you might not have enough to power it. Remember, you can run an attack drone and defense drone on the same power supply! The drones stick around, meaning reactivation doesn't cost anything - leave your attack (if you have one, or whatever) drone active until there's an incoming volley, and then switch power to the defense drone, shoot it down, and switch back. If you are particularly aggressive, two MKII attack drones are truly a thing to watch.
Drone Arm, Scrap Arm (You can sell both before the final boost, obviously, and spend the cash elsewhere), Hull Repair Drones, Weapon Pre-igniter, and Weapon Autoloader are all pretty good additions to the build.