My favorite is now the Nisos, Federation B. After some success with the Osprey, I started to find it prone to failure/wasteful damage in early zones, vulnerable to system shots and missiles. Now after the first try loss, I'm 3 of 4 with Nisos.
Nisos is better early in a number of ways. Shorter cd laser (and superior to the 1 energy, 2 shot laser you find in stores) and the efficient Leto Missile (in battle, not on your missile count). Having the artillery at level 2 is a significantly better fallback than artillery 1.
Idk if the Leto Missile is underrated, but I find it very useful/versatile and keep it up to the boss some games. I hate basically all other missile weapons and avoid using them if possible (some bombs are okay. The Leto's low power req makes it easy to toggle on and off whenever needed, as a supplementary weapon system. In many battles you are fine without it and can rely on artillery, so it fits well as a little extra oomph vs certain enemies (primarily high offense ones, where you need to damage their weapons quickly)
You even start with one SURPLUS energy, with the Zoltan. Very few (any?) other ships have that edge. So you can do a quick + 2 engine upgrade and handle it fine (with oxygen management). I think with the Zoltan, artillery, and decent weapon systems Nisos just has a lot of starting value.
Sure, 3 crew is sorta a weakness, but that's really all you need to overcome.
Idk if it's just chance, but I seem to get the random event where you go down to the planet and see the aliens a lot, and the Slug lets you automatically get an Engi. Also the madman event seems common. So I get pretty good value out of Slug blues.