Well, again, my problem with the Engi ship is that if you want a second weapon, you have to buy it, then power it. That's around 40-60 for a cheapo weapon, plus around 90 for two weapon slots, and then another 45-50 for the power. The main gun doesn't actually do damage, so you're relying on drones.
I dunno, it seems like it's really hard to get the right stuff to succeed with the Engi. I guess I should go back and try the original Kestrel for a while
Its not. You don't really need to rely on weapons.
Drones are pretty cheap, and 2 attack+1 defense+ion blaster is very doable by the end of the game (or if lucky 2-3 areas earlier), which is enough to take down level three shields on its own, while keeping you safe from missiles.
If you can complement that with a teleportation pad then you have very powerful offense (not as powerful as you can get with a dedicated offense with multiple weapons , but the missile defense drone and the fact that you can put everything on auto so you can focus on your boarding party pretty much makes up for it), while being able to have (if you can build the shield up to two at least) pretty decent defense.
Also, keep in mind that for the engi ship a missile or some teleportation weapon would probably be better then another regular weapon (since due to the drones its a bit sporadic and when the shields go down).
Also, keep in mind that if you can get the drone retrieval ability you can just throw all your drones out to fight every battle, which makes you very powerful and without any real resource limitations.
That said, I haven't won with the Engi ship (due to me screwing up a bit during the boss fight (like not knowing they have improved blast doors and teleporting my rock+mantis boarding party into their healing room to try to shut it down, leaving me without good offensive options for the next stage of the battle), or running out of missiles for the second phase) but I have a ~50% chance at this stage to get to the final part, which is better then I get with the Kestrel.