Playing 1.06: I restarted and I've been using missiles till level 9ish, as the Utopian (computer) ship. They've also tweaked balance, might be worth retrying, Lancefighter.
Without going out of your way, you always have a 95% tohit chance, and if you don't, the booster will take care of that, so missiles always hit if they don't run into a missile swarm first. Angle seems key for taking down certain enemies.
I've been running as the smallest ship class for most of the entire first sector, thanks to a lack of engines and thrusters. My general setup was:
Heavy: Drive, Power Plant (or Armor if not available very early on), best missile I could find
Medium: Deflectors, Medium Armor (critically useful), Manual Ram Accelerator/Battery Bank (when energy costs for missiles go up to 30/shot)c
Light: Battery Recharger, maybe one other green module, crew.
Keep your speed up, talk to planets for the recharge, and you can do a decent job of clearing things out. It also might just be RNG, but the "small" maps may be easier than the tiny, with less of a level jump for adjacent systems.
I do need to keep another weapon on hand for when a "200% explosion resistance" boss comes up.
My main complaint is that the bigger maps are, the smaller they feel. Basically, exploring feels like punishment rather than reward thanks to excessive fog of war. After you've seen them, derelicts, storage, pocket dimensions, ancient recharge stations should be marked on the map until they no longer exist. When you're in a new system, you should at least be able to see the locations of the planets on the full map screen, even if you can't fill in the details. Detailed exploration should be encouraged not required. Even if you're allied with a race, you cannot actually help defend their planets until you stumble around in the fog to find them.
I can see this getting more interesting later on, but the constant exploration with no shortcuts makes me perfer Space Rangers 1/2 atm.