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There is also the distinct possibility that, once a ship like Corrupter shows up, it doesn't much matter what you think of the Empire as they are here to light you on fire from space.

Considering what the Malevolence does (Ionize the surface of an entire planet and kill everything/disable or destroy whole squadrons with a single pulse) Subjugator is a pretty good name.

It also looks weird to call a powerful ship-class meant for heavily offensive operations something like "Resistance"-class or "Petting Zoo"-class.

With the Recusant-class it's easier, because they're made by local populations who want to resist and withdraw from the Republic.