But vanilla was so... vanilla... and so rather than work on my own mod, I downloaded Infinite Space, fired up Grognak's mod manager, and a dozen hours or so later, I have broken the game.
*Note, I am also using Kieve's Obsidian Cruiser mod, because the ship is absolute eye candy. That, and the starting weapons kit it comes with helps you farm scrap really quickly.
Overview:

Augmentations and Spare Parts/Alternates:

This build takes no thinking at all to obliterate any opponent, the toughest opponent is probably the Pirate BB.
You just hyper in with weapons hot, if they have Zoltan Shields, you launch 3 Advanced Anti-Ship Drones, which chew through shields pretty quickly. Then you unload your massive 12 damage, 6 multiple independent warhead salvo into their shield room, and then cut through 3-4 rooms with the Advanced Beam. With a moderate amount of skill and patience, the Advanced beam is almost always 8-9 damage guaranteed- and with opponents that have clustered room design, its possible to hit 6 rooms for 18 damage!
If they somehow survive the alpha strike, you either wait for them to launch a heavy salvo and Cloak at 1 to dodge incoming hits, or Cloak 3 to reload all your weapons and repeat your alpha strike- and thats if 3 drones don't kill the enemy ship by themselves- if you've hit the engines or disabled the piloting station, 3 Advanced Anti-Ship Drones really melt the opponent.
With 3 crewmen at 6/6 mastery and 5 crewmen at 5/6 mastery (none of them are more than green, or veteran at weapons officer), losing a crewman is far more painful than getting hit a few times or losing a few hundred scrap.
With Zoltan Shields boarding is almost never an issue, since you can roflstomp your opponents with the silly firepower in this build and use cloak to supplement/preserve the boarding immunity, and even 4 Zoltans in a room can overwhelm 2 Mantii, given Medi-Bots. If there weren't events that caused boarders to appear on your ship despite the Zoltan Shields, I'd consider switching to a 6 or even 8 Zoltan build so I could power all my Drones, Weapons, and still max my Shields without setting Oxygen to 0

Thoughts:
Because of how Defense Drones tend to focus-fire one missile at a time, even if an hypothetical opponent had 3 defenders you'd almost certainly still get 1-2 hits on their shield generator unless the RNG really hates you (happened to me once or twice). Which reminds me, I need to ask Kieve if a beam-based defense drone is possible; i.e. instant-hits against missiles with 100% accuracy, with no/negligible projectile travel time.
Infinite Space needs to give its 'boss' opponents more HP.
If a very powerful and accurate defense against missile-opponent was introduced, you could always switch to TP bombs, Ion or Breach. Fire takes too long to work, during which you get shot at, although it is quite hilarious to set half the enemy ship on fire and burn everything.
Even though bombs tend to be far more power-efficient for damage than Missiles, no bomb system fires two bombs at once- and thus they get screwed over far more often by RNG. I've tried quadruple Bomb builds with this mod and in vanilla, and all too often you get triple or even quadruple misses. I've yet to get all 6 Pegasi missiles to miss, though.
EDIT: Resized images.