I just beat the game on easy and I figured I'd post some tips that I picked up on.
The hardest part seems to be the last boss. It's a 3 stage boss fight that gets progressively...different. But there is a few things you can do to make the last fight more managable.
Namely, try to get:
Cloak level 3 ( the cloaked firing module is not required ). Cloak is immensely useful, probably the most useful thing in the entire game. The reason for that is that enemy weapon systems generally don't charge while you are cloaked. If a volley is incoming while you cloak - no problem, cloak adds 60% to your dodge ( which, combined with your engine upgrades and pilot, should result in 100% dodge ). Your weapons however, keep charging up. Drones won't fire on you either.
Boarding Drone. If you pick the Kestrel and pick up the drone system fairly late, you end up with something like 20+ drone parts. Shooting a boarding drone seems to always hit ( unless they have a defensive drone, or health-bar shield !! ), guarantees a breach and kicks their crews ass - also no cooldown or anything. As soon as it dies, just fire the next. As a added bonus, it can be used while cloaked without adversely affecting your cloak duration.
A way of beating through a level 4 shield without relying on missiles. If you are fairly missile oriented, there is a chance that you get utterly boned on stage 2 of the boss fight, as he uses a level 4 shield + a level 2 defensive drone which shoots down both lasers and missiles at a annoyingly fast speed. I had the starting burst laser lv 2 as well as a hull laser level 2 and the starting rocket launcher. I had to fire all 3 weapon systems simultaneously ( as well as the boarding drone ) and i'd barely get 1 hit in on the shield and the boarding drone to land.
As for the actual strategy, everytime the enemy uses a special attack, make sure to cloak. Generally, try to cloak as much as you can ( preferably right after you fire a volley - so they your weapons can recharge without danger ). You can avoid the majority of damage using cloak. The stage 2 boss fight has a special attack where he releases like 5 additional drones for a few seconds - cloak avoids that entirely.
Keep your boarding robot active on their ship, and focus on bringing down their level 4 shield first and foremost.
Good luck ! I hope these tips helped. I wish I knew about all this before hand, as it renders some builds useless ( or rather, unwinnable ).