I think an armored colony ship should definitely have some kind of rather high cost for while-it's-in-the-field just so you can't have nearly invulnerable contingency plans lying around. The regular colony ships go down to a stiff breeze, after all, so stocking those up is kind of not amazing (unless you hang out in deep space and throw down a command station when things cool down or something).
Do something like a high energy cost that goes away when it starts building or something.
Otherwise I have no problem with armored colony ships. They just shouldn't basically be a straight upgrade of regular colony ships.
...ooh! Maybe you could have a variant of the colony ship that instead has a cloaking device. Tachyon beams knock it out, but that's why you knock out tachyon guardians then slip your colony ship through without worrying about cloaker starship woes.
Why are you worried about contingency plans? How much need for an emergency colony ship is there? A destroyed command station can be rebuilt by a rebuilder and those are cloaked already. Colony ships are for planets you haven't settled on before, that's rare enough and I can't even think of a situation where settling something is part of an emergency plan.
All the solutions in the player toolbox require intensely micro heavy solutions.
Load into transports (for short term solutions) or use cloaker starships (for heavily neutered solutions).
Both of these soltuitions basically cover up a very basic fact of colony ships: anything can kill them, period.
For most situations, that is fine. Like how tachyon drones (with enough micro) are fine for your tachyon needs or unusual situations.
However, tacyhon needs have more options. Because some players don't want intense micro.
For the same reason, I don't see how colony ships can't have an option for less intense micro.
This isn't a free option. You are paying the very real K cost for an expanded strategy tool box.
