It depends where I'm at in the campaign. Scrounging for scraps at level 3 is a completely different game then outfitting a fleet to take out a high-level bounty or chain-battle pirates in a double-bounty system. I'm all about the high-tech ships and tend to like to play Starsector like an arcade game, as Vanshilar mentioned, so for me the keys are high maneuverability, high speed, a good shield, and decent firepower.
In the early game, and since the early days of Starsector when they were rarer than diamonds, I've always liked the Tempest. Now they're as common as Coke cans, but I still make getting one a priority in the early game for my first chosen flagship. Hardened Shields, Resistant Flux Conduits, and the Remnant weapon or overpowered mod weapon of choice, whatever I get lucky at a black market or the highly shielded cache with. Even with random dual Phase Lances or Mining Blasters, piloting the Tempest doubles the power of my early game fleet when I'm still limping around with the D-Modded Hammerhead from the tutorial as my largest craft. Even after I'm using cruisers and battleships, I still keep a couple of Tempests in my fleet for pursuit duty. You wouldn't believe how many kills two Tempests get in the pursuit auto-resolve against a fleeing pirate armada in a bounty system until you try it, I regularly see them take out twenty times their weight in pirate ships.
The midgame comes whenever I can first find and afford a Medusa. Still fast and aggressive, the Medusa has enough durability and a tough shield to compensate for me making a few mistakes, so it's a slightly more relaxed and deliberate playstyle. The Medusa can be a shield-tanking overgunned monster for a few minutes with Safety Overrides, but I generally find that it requires investment of Story Points to fit in everything I want in a SO Medusa build, so I normally use it without SO until I find my exact choice of weapons.
My absolute most-used craft in the current vanilla version has to be the Aurora. My first Aurora is WORTH sinking Story Points into, because I will most likely be using it into the endgame. This overfluxed highly shielded monster imbalanced mod ship, which for some reason has been in vanilla for a decade, shows exactly what Safety Overrides can do. I like to cram triple Heavy Blasters and Hardened Shields into it, anything else such as the side medium mount and the front four small mounts, depends on what mods I'm running and what was in the shielded cache. Antimatter Missiles, Shock Repeaters, Minipulsers, and especially the Disintegrator, any or all of those will determine my exact build. Another heinous and ruthless trick is to stay as a frigate swarm into the midgame, but fly an Augmented Drive Field Aurora as an ultrafast cruiser flagship that, even without SO, can generally solo any fleet that can remotely catch it.
My favorite "new" craft in our current version is the Eradicator. Cruacious and Vanshilar already mentioned it. I'm generally only going to actually fly one if I'm using a full cruiser fleet and haven't yet found an Aurora, but it's my favorite to fill out my fleet and make a battleline with Steady or Aggressive officers. I don't care for the pirate version, the Burn Drive lets the AI get itself into trouble more than I find that it ever helps, but the Luddic Church version with Accelerated Ammo Feeders is amazing. They're trivial to find and easy to replace even if your character build cares about losing ships, since if you follow the main story line the academy will constantly send you on ransom missions to Luddic planets where they sell this variant. I like to put Integrated Targeting and two HVDs and One Heavy Mauler on it, a main line of these is useful against any threat in the base game and a lot of overpowered mod content. As much as I like to break the AI over my knee with unfair energy weapons tricks, Paragon swarms and the like require millionaire income, which I consider basically postgame. Most of my lategame fleets until I've beaten all the hypershunt fights and gotten a few max-size colonies are going to include four or five Eradicators to provide a cheap, dependable, decently armored, long ranged hail of bullets anywhere on the battlefield.
