My problem is that because there are so many options now, I often end up with something that kicks ass everywhere except for the final battle. Totally my fault of course. It's probably partially due to the fact that I haven't figured out how to master some of these systems for the flagship (yet). Can still do alright with the "traditional" combo of good shields, defense drones and good engines.
Yeah, you do need to figure out what works well together and what is more important than what, but once you do, the greater selection makes it easier.
Cloak helps but isn't essential if your shields/engines are up to the task.
Unless you got a lightning-quick killer gun combo early on, you usually need something to counter missiles, be it a cloack, hacking or defense drones.
Otherwise, you'll spend too much on repairs.
By the way, does the Ion protection augmentation work against those systems that send out random ion blasts? I haven't tried it, but if so that would be one way to not get hammered so badly in those. Once I got my shields AND weapons taken out, while the enemy ship could still fire and their shields were up! I ended up winning with a boarding party though.
Probably, though I'm not sure if it's worth it given the likelyhood of encountering such a sector facing a killer ship.
Definitely wouldn't pass an automated reloader for it.
I just byte the bullet when I hit a ion blast sector and pray I don't get too unlucky (in terms of which of my systems get ionised, which of his systems get ionised and how capable my opponent is overall).
I figured hacking would be cool - and it is - but if you have no bombs and no teleporter and are relying on lasers/ions to bust through the flagship's shields, then the second phase can get a bit annoying as it can be a pain getting a hacking drone past their defenses. It can be done, it might just take some time...
Yeah, the second incarnation sucks for hacking and is the main one you can't depend on hacking for.
I usually divert power away from hacking and into other systems for the second incarnation unless I get lucky and destroy his defense drone with a volley of fire.
If you're extremely good with the timing, you can probably get your hacking drone through by firing a missile or two just before it, though I admit I haven't tried it, but it should work in theory.
I also believe there is also an augment that either disables or seriously reduce the effectiveness of defense drones. Haven't tried it yet, but it seems like a good combo to have with hacking.
And finally, it just occured to me that using a teleporting bomb that does 3 points of damage or more to disable his drone system will also allow you to use hacking on the second incarnation.
Personally I LOVE the vulcan cannon. As long as you have enough capability to avoid damage long enough (good engines, defense drones, cloak, and/or good shields), then you just sit back and watch it rip through the enemy. It's a god-like weapon in my view, as once it's at full speed the only thing that stands a chance is a ship with 4 shields and a high-level engine, and even then eventually you'll get lucky.
Problem with that is that the final boss has some insanely good combos on the 2nd and 3rd incarnation.
In the second incarnation, he has drone surge + triple missile launch and in the third incarnation, he got power surge + triple missile launch.
Cloack will negate one of those things (ex: either the triple missile or drone surge on the second incarnation, but not both as the timing simply won't coincide).
Your evade/shields will mitigate those threats, but he'll still punch through and if he compromises the wrong system (ie, engines, weapons, shields or cloack), you can get royally screwed.
So, I find the best defense is a killer offense, especially for the third incarnation where your must punch through his shield to teleport.
I mitigate the luck factor to a minimum, by giving him at most one free missile/drone surge/power surge volley.
The vulcan cannon is just too slow and can't cope.
I mean, maybe if you got like level 4 shields, good engines, cloack and some defense/disable drones, you can weather a prolonged battle while his missile launcher is intact but that seems like some serious investment when you can just ditch one level of shield and the drones in favor of faster weapons.
Just out of interest which C layouts have you unlocked so far? While some aren't that exciting, I find most of them to be pretty cool. They all come with clone bays for a start (which I've now warmed to), and there are at least two that provide unique challenges. Most (if not all) seem to have better airlock layouts for quick venting which is always a plus. On top of that most of the C layout ships have cooler looking hulls (except the slug one which is this disgusting bright yellow for some reason - but at least it's not missing a med/clone bay!).
I got the C layouts for the federation ships (starting ship, cruiser & stealth ship) + the manthis I believe.
In particular, I found the C layout for the stealth ship seriously lame as it got no cloack.