Currently the CW fleet missions on CSCs are implemented in an older method than the current standard. This means that in order to modify the carriers (as shiptypes), you have to override all the missions as well. This adds thousands of lines of additional code to a simple override.
When possible, the missions should be recoded in the current system and separated from the ships themselves so that modification is easier.
Specifically, CSCs should use mission types and the Flight Deck should use rpgMissionAssignment. This way more missions can be added in via extensions.
I've been thinking of doing that for a while. It's definitely an important thing to do, given that having a vanilla example of the new system would be quite useful.
Militia, Korolov, Commonwealth mining, and other old Commonwealth missions should also be updated if possible.
I did rewrite the Korolov station and missions as part of my KorolovMissions mod. Currently there are few extra enhancements (communicate with freighters, wingman encounter, hooks to the rumor framework I was testing) but these can be easily removed. Feel free to take any parts which look useful / let me know if you'd like the core-rewrite parts separated out.
Fixed in 1.8 Alpha 1, thanks to @giantcabbage.