So I flew this absolute leviathan into battle with the final boss; all shields up and maxed out hull. I've taken on the boss multiple times before and failed miserably every time; the very first time I was flying the stock ship and pushed it to it's third form. This was my third attempt at the game. I was on my last legs and it destroyed me in seconds. Since then I've never gotten past it's shields on the first form. I fly the Engi Cruiser using Ion cannons and drones, and a Halberd beam when I can get one. I usually take out the huge Mantis Aggressors with a flawless, <30 seconds victory; undamaged, no deaths, no wasted drones. I play without using the pause button.
I imagined that using a triple-Ion cannon along side a stock Ion cannon would get me past at least two of it's shields, allowing for a well timed line-up of those two, an attack from my Combat drone and my halberd beam to deal some real damage to the shields, then take the fight to it's FTL drive to stop it dodging and pick apart it's weapons systems. The resulting battle was maybe 10 minutes long and tedious; I never got past more than 3 shields.
I'm guessing the first thing I'll be told is 'Use burst lasers and no Ion cannons' but Ions are the only way of keeping a ship's shields down once they're down with the Engi cruiser, and they're the only tactic I can work almost flawlessly.
Anyone else using Ions and the Engi cruiser for a shot at the boss? Before anyone says I should have spent the scrap I had saved up (~720 by the time I actually got to the Boss), I was using every single power bar there for dodging, shields, Ions, guns and drones.