I would really love to see the nanobots just getting added to the hull cruisers and battleships have.
The removed nanobots will be converted to the normal ship hull. There would be no armor lost at all.
Pros:
Repairships are actually viable for the whole duration of the fight and after.
For such a big vessel, seeing how far you are to destroying it is a nice thing to have.
Cons:
Armor upgrades are having less impact(might be a plus for some) because the nanobots are now equally repairing for all of them. - Might be I misunderstand how AUs work here.