Couple things I thought might be worth mentioning... First of all, the arty beam counts for the Slice and Dice achievement (it decided it was going to just slice an auto-assault drone in half, and suddenly I had the achievement), and for whatever reason it counts towards the experience of your gunner whenever it fires (even though, so far as I can tell, the gunner's expertise has no effect on the artillery beam).
Just tried out the Fed Cruiser type B, and on the very first run had a strolling victory. Never even had particularly good weapons; when the boss came I just had a burst Mk.II and dual laser to beat down the Zoltan shield, then switched over to fire bomb for taking out the weapons. Everything else was all on the Dicklaser.
No cloak, not even hull drone this time around. Just a defense mark one. Never left the green zone health-wise until I shut down all weapons on the final form to just let the fires sloooowly kill it, because it was going too quickly... That's when I earned the "Astronomically Low Odds" achievement and started getting a bunch of damage, so I decided to turn the ejaculaser back on again.
I quite like the Zoltan ships. Particularly the type B, actually. Sure, starting off with no real shield is a pain, but the ion blasters you get allow you to take down most early enemies and suppress their weapons while slicing them apart with the pike beam. Any initial hits you would have taken are blocked by that delicious Zoltan shield, which helps you get past the early-game missiles with nary a scratch. Also, I think the Noether has a slightly better layout than the Adjudicator.
But again, my experience thus far with the Fed cruisers has been that they're effectively easy mode. With them, the best offense really is a good defense.