I'm fairly new with this game. Just played 2 months ago and currently I'm in level 73. From my observation regarding capital ships, seems each capital ship is better run with their side. Such as Tarki...
Scoundrel ships don't have faction synergy with any capital ship so just use is with whatever you like.
While there are some faction synergies among ships, they are generally not as crucial as in squad play so you'll see a lot of mashup fleets based more on ship ability synergy than faction synergy. Classic Biggs, Tie, Vader lineup for example is all about the target lock mechanics of the ships involved.
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