There are some things you can do if you want to balance it out a little bit. You can put a cap on factions by giving money penalties if they get over a certain number of provinces. So for the Greeks if they have 5 or more province and treasury greater than a certain amount you can give them a cash penalty. Same goes for the Ptolemies. You can also try to change the AI "mentality". So making the greeks into a "fortified" faction may make them more of a defensive faction.
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