Bodyless: the zoltan cruiser is easy? i have yet to beat the game with it because the layout is crappy and the starting crew sucks at fighting melee.
It has 4 weapon slots, awesome free HP/protection from the Zoltan shields that gets you the starting advantage and free energy from the crew.
What's not to like?
Sucking at fighting is not new to that race. By the time you play them, I'm sure you'll have devised a couple of tactics to deal with an overwhelming boarding crew (oxygen starve them, force them to fight in med bay).
In a way, you get a leg up at the start, because they need to take down your Zoltan shield before they can board.
Take out the transporters at the beginning if their crew is that intimidating.
Bodyless: mantis and slug cruiser are strong because killing the enemy crew nets you more scrap then destroying the ship.
Manthis Cruiser is strong because boarding is an awesome strategy against the relatively inept AI (a human player would be a lot better at dealing with your boarding crew).
You don't need to penetrate the shields, just beam up the crew at the right spot and take out a system for free right there.
Even better, most fights will end once you takeout the crew so you have a fast way to victory there as well.
Also, the last boss has his main weapons isolated in closed rooms, so you just need to send 2 crew members over to each gun and take it out for the remainder of the battle pretty painlessly.
Bodyless: about the stealth cruiser...dont just activate the stealth when is ready. use it do dodge enemy shots by stleathing right after the enemy fired. this makes him waste the shot and stop him from recharing his weapons for some time. getting a shield early is importent, just pray you dont get many enemies with beam weapons.
I'm aware of the tactics. I did defeat the final boss's first 2 incarnations with a stealth ship.
There are a couple of issues.
1) If you do not kill or disable the enemy ship in 1 shot, you have to deal with return fire because stealth recharge is slow.
2) Like you said, at the beginning, you're in a rush to get shields. That diverts resources away from getting killer weapons which this ship badly needs because it's starting weapons are pretty much useless against shield 3 and above.
Also, the fact that it has 3 weapon slots means that you need to find level 3 weapons to get the killing firepower you need to take on the final boss.
And unlike the manthis ship, you're not a natural boarder (which is an alternate way to quickly get at their weapons or their shields).
And finally, you can't wait at your leisure to cloak when the enemy ship has drones.
Bodyless: Dodging the flagships shots this way is awesome but the federation crusier cannot get any stealth. you really need a defense and hull repair drone to survive imo.
You sure it can't?
I tend to get stealth relatively early on for most ships and it seems like something I would have noticed if the Federation Cruiser couldn't have gotten any stealth.
Bodyless: engi cruiser is kinda soso because attack drones just dont cut it against the flagships and the mark II drones arent much of an upgrade.
You combine drones with stealth and it does fine.
Also, you can backup your drones with weapons (the drones were not meant to do all the work by themselves).