Since this was written 3 months ago there are now Skirmish hulls as big as anything else, so they can benefit from this info now as well. At the time Siege hulls were the biggest in the game.Optimal improvement of large Siege, Garrison, and Skirmish hulls
I'm starting with Siege hulls because they have the highest HP, and if you have to spend repair time and/or coins, you want to spend it on the ships with the highest armor ratio to make the most of every second of repair and every coin. If you CAN use your siege hulls in a non-siege target, do so!
Garisson hulls and the larger Skirmish hulls have very high armor compared to Assault hulls as well, so the same improvement techniques will work, but the gains will not be as dramatic as with Siege hulls.
The most important thing to remember about the new Siege hull defense is they have gigantic base armor now, so you need to completely ignore whatever armor points that armor adds and focus on the other benefits.
The most powerful Limited armors are your Charged and Zythonite D6. Charged armor HP pools vary, but the largest are around 250K or so, and the D6 armors give you 50K. Both weigh very little and have Survivability stats, but the armor they give you is quite useless on large Siege hulls and a waste of these otherwise very powerful Limited armors. Save these for much smaller boats, they can become ultra-powerful using these. The Ballistic/Radioactive non-limited charged armor IS useful if you want to use your Siege hulls in Siege targets because this particular type of charged armor adds both Ballistic and Radioactive Survival, as well as a tiny amount of Deflection. YES, deflection still exists. The mechanic appears to have changed and it is still very beneficial in small targets. More on that later.
Heavier armors that add both armor points and Survivability are even worse, because you get fewer armor points which are useless on these monster hulls anyway, and they weigh a lot, and add repair time which will LOWER your armor ratio, and you definitely don't want that.
Ferrite armors will add two Survival factors each, and no extra repair time, and there are no class restrictions on them. However, the 100K armor is going to be pretty pointless, and they weigh a LOT. These are a lot more useful on classes of hulls with much lower base armor but higher weight allowances, as well as some classic hulls with large weight allowances but very low base armor. Don't waste the weight on your siege hulls.
Believe it or not, your best choice for adding survivability to these huge hulls is the smallest junk zynthonite armors you can throw on. These are the things you find in tier 1 and 2 prize stores in raids and in cargo fleet drops. They add very little armor, which we don't care about anyway with millions of base HP, but add very little weight and repair time, which matter a great deal. Another good thing about these tiny and apparently worthless armors is there are no ship class restrictions on them at all. Put on whatever armors fit the targets you want to hit. Using the Eradicator as an example, even if the junk armor increases your survivability vs that damage type by just 10%, it adds about 3 million extra armor points for that damage type. Another bonus with these tiny armors is your Survival specials don't add weight based on a percentage of your whole ship weight, they add weight based only on the armor, so your armor special will add very little weight to your ship. Depending on which ones you are able to find, they will weigh either 67, 100, or 133 tons. Heavier armors will not add much more survivability but will come with a lot more repair time which will trash out your armor/repair time ratio. Use the smallest ones you can find that fit the damage type you want.
Armor specials are pretty straightforward if you want to hit big targets. Put on whatever dual type fits the target you want to hit.
If you are hitting smaller targets, selection of armor specials gets a bit more interesting. A reinforced armor type might be the best choice due to the fact these still add 50 ship and structure deflection. More experimentation is needed, but it appears that not only does Deflection still exist (just not as a base value on hulls anymore) but the effect is very dramatic vs smaller targets because it appears to be calculated AFTER the Survival factor is subtracted, and not before like Resistance was previously. I equipped a Battle Barge A with a reinforced ablative and sent it into a lvl 68 Research Garrison. It took no damage whatsoever. The same thing happened with a Punisher equipped with 3 charged ballistic/radioactive armors. Even though the charged armor pools did not play into the Garrison damage types, the 30 deflection had the same effect. No damage was taken from turret or ship weapons. Hitting larger targets with these ships resulted in damage taken, so the effect only applies to smaller targets. However, damage dealt to player ships in Assault targets is much less. More on that when optimizing defense for these ships is covered. If you do use a reinforced armor special, it only has Survival for one damage type, so if you want the other damage type in the targets you are hitting covered, use the small armors for the other type and it will be more even.