My suggestions are RP-oriented. First of all, I think you should consider "expelling" populations towards hostile territories. This can be done by console commands, using "add_population [city name] [amount]" with a number in the minus to take the population away and the same amount to take then to another city. The rationale behind this, is obviously the fact that many citizens would already leave in fear of being treated harshly, or just a tool for lowering the possibility of rebellion. You just use the command twice, one to take population out of a city and move it to another. This is good as a subtitute of extermination, which I only use when absolutely necessary or RPing a general's selfishness and hatred towards another faction.
Another suggestion I have for you, is to RP your change from a tribal confederation to an Empire. Change your governmental buildings into others that have a more "Empire" feel to them, with corresponding bonuses and penalties. Make more units available to you, and focus more on infrastructure than being plain expansionistic. The latter will cause lots of problem in the long run, so try to build up slowly and RP as much as you can to enjoy your campaign to the fullest.
Maion
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