What do y'all think are the best missiles that only take up one slot? I'm thinking about the generic inquisitors with passive sensors for locks, and then all they need is a missile. Anyway, with passive sensors maybe allowing low i ships to take more munitions, what do you think?

Depends what you're after them for, I guess, which depends on how many of them you have and what's in the rest of the squad.

• As you've described, probably Homing, Ion or Concussion
  • Passive Sensors are all about being able to grab a target lock at long range on an enemy ship with a higher initiative than you.
  • That suits range 2-3 missiles.
    • If you only have 1 or 2, take homing missiles, because they work well 'on their own', giving the TIE/v1 a nice bite at a range where it's 2-dice primary popguns are pretty ineffectual.
    • If you have several - 3 or 4, or even 5 if you're prepared to take Barons of the Empire instead, Ion or Concussion become more tempting, because those missiles are more important fired en masse - Ions because you need 2+ un-cancelled hits to ionize a target for a range 1 'pounce' with primary weapons, Concussions because you need to hit a ship for damage then hit it again to flip the card with the Concussion effect.
• Cluster Missiles are perfectly valid choices for the TIE/v1
  • It's a cheap 'bin' of 4 3-dice attacks at range 2.
  • Inquisitors can make better use of the bonus attack option than most by using their force token
  • I wouldn't feel the need to use passive sensors since they are range 1-2; move into range 3 and lock, and your opponent will generally move from there into range 2 where you can shoot them. By comparison, Fire Control System is cheaper and means you don't need to keep locking again and again, opening up your awesome reposition/link/focus for knife fighting.
• Proton Rockets are also good choices
  • Since they're a focus, not target lock, missile, you don't need fire control or passive sensors to use them.
  • Interestingly, an Inquisitor with Supernatural Reflexes and Proton Rockets is now 50 points on the dot. That's 4 very manoeuvrable and tough ships, each able to do a pre-move boost or barrel roll, followed by a speed 1 bank or turn, and have focus/evade on agility 3 and a 5-dice 'boresight' shot on anyone dumb enough to be caught there.

There isn't one. You're reliving wave 1-6 from 1.0, the game evolves in stages. Wait for them to make more powerful missiles, or drastically undercut the existing ones.