Minor balancing issue: Some of the Citadel ships are consuming too much fuel to be feasible to use.
e.g., the Modem-class destroyer consumes as much fuel as a capital ship. The Stable-class Freighter (frigate-size) consumes almost twice as much fuel as some cruisers. The Monolith Battleship consumes a whopping 50 fuel per lightyear, which is up to 5 capital ships worth of fuel. There are probably other Citadel ships with similar issues, but I haven't checked all of them yet.
I think these ships are intended to consume more fuel so that they're more expensive to run (but also stronger than) vanilla Starsector ships. However, the other stronger-than-vanilla ships from other SS+ add-on mods don't have this same handicap. So for the same fuel costs, you can field many times the number of ships from the other mods each of which is equally strong, if not stronger.
Normally this would just be an imbalance or an annoyance, but once you consider the x2 fuel consumption multiplier, each of these super-guzzling Citadel ships begin to cost even more upkeep in comparison to vanilla and other mods' ships. Essentially, using them is just choosing to cripple your own finances.