That's not very helpful, is it?
The problem is that, whether you create one or two rebel factions, the "rebels" would still be an artificial unit. If you turn Athens' colonies/allies into a faction, it will actually behave like a single nation rather than independent cities. Since EB is about realism, this is undesirable.
Also, the "rebels" aren't just pirates and brigands, in fact most of them aren't even rebels. They are minor factions that could not be included due to limitations in the engine. As such, it would be realistic to be able to negotiate with all of them, but again engine limitations don't allow this level of realism. Splitting them in two, so you can negotiate with part of the "rebels," seems a poor simulation of that.
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