Could it be that this mod has a really bad performance impact? I've recently started a 0.98 game including this mod (admittedly I don't even have a vanilla baseline, because I never play vanilla). Since I got FPS problem way before any colonization or even just invasions started (so maybe 2 hours of playing time), which I never had with 0.96, I got VisualVM profiler. I found that second_in_command functions are way up there in CPU time usage.
Here are some example (the percentages are percent of total CPU time without sub-calls)
second_in_command.specs.SCOfficer.getSkillSpecs () 12 192 ms (4,7 %)
second_in_command.specs.SCBaseAptitudePlugin.getOriginSkillSpec () 7 786 ms (3 %)
second_in_command.SCUtils.getFleetData () 6 500 ms (2,5 %)
second_in_command.SCData.getAllActiveSkillsPlugins () 4 904 ms (1,9 %)
second_in_command.hullmods.SCControllerHullmod.applyEffectsBeforeShipCreation () 3 902 ms (1,5 %)
second_in_command.specs.SCOfficer.getActiveSkillPlugins () 2 400 ms (0,9 %)
There are also functions that don't use the CPU much on their own, but constantly call something that takes a lot of time (times/percentages are including the time of sub-calls):
second_in_command.specs.SCAptitudeSpec.getPlugin () 5 697 ms (1,5 %)
java.lang.ClassLoader.loadClass () 4 100 ms (1,1 %)
java.lang.Class.newInstance () 1 597 ms (0,4 %)
Self time 0,0 ms (0 %)
And these are not all of them. That's easily 20% and more in CPU time for a mod that shouldn't need to do any calculations unless you change skills or maybe the environment changes.
In the hopes that I'm using VisualVM correctly, could you please look into that? Maybe do some caching in the right places?