Well also with the WRE you can expect a revolution to occur within the first few years so simply decide which cities will do so by adjusting the garrison, tax rate and religious aspects. Obviously try to limit the revolt to about five cities and then simply attack them and eliminate the populace which should decrease future problems there and also generate some cash.
Oh, one bit of advice is to also strip these cities bare of their buildings which will give you cash and also taking out their military buildings means you won't face a revolt with anything higher than a peasant unit.
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