Swarm looks pretty good, actually. It is ultimately the fastest missile in the game, which means you can potentially strike the enemy with 1 or 2 piercing damage to take out their missile before it fires (e: actually I'm not sure if it hits early enough to stop an Artemis). It can also sneak 2 damage past defense drones (I think?) at a rate pretty comparable to the Pegasus Missile for 1 less power, or 1 damage past a defense drone before any of the big missiles are ready to go.
Also the Virus event is so good that I go to Engi sectors whenever I can.
Zoltan shields, Zoltan, Mantis, Lanius or Rockmen crew are really hard to beat with boarding and medbays or cloning bays are pretty nasty too. Higher level doors are also not fun. And I find that when the enemy boards YOU, you need your boarding Mantis's on your ship killing them instead of ripping through their crew while your own ship burns.
For Zoltan shields you just need to shoot at it with a weapon/drone, like with any other ship. Zoltans are still pretty pathetic when it comes to fighting even with their explosion, it doesn't really make up for their reduced HP. Lanius only appear in one sector which you can usually avoid. Rockmen still usually lose to Mantis in a 1v1. Mantis are a bit trickier, but you can deal with it by double teaming them or just teleporting back and healing.
You do of course need to take out their healing system, that's usually best achieved by getting some kind of bomb or any other kind of offence that can hit a bit of damage through their shields.
Enemy boarding parties really shouldn't be a problem if you have improved doors (either by purchasing the upgrade or having someone man the system). You can just drain the room they're in, then drain the room they're about to move into, and keep them locked in a cycle of suffocation. Alternatively you can drive them towards your medbay where basically any species will be able to take them on and win. Unless it's a very serious invasion you should be able to fight it off without engaging any of the boarders in actual legitimate combat.