You're probably playing the wrong factions to notice the missile changes (though you could use horse archers as a mobile reserve for internal security as the Seleukids), but they're pretty significant. Nothing has been changed on the melee side.
Glad the scripted Ptolemaic response makes them less of a pushover.
Can't speak to the AI behaviour. Weird that it's chosing to move it so far south and ignoring the far more important and richer city to the north.
There's far too much money far too easily available in the game. A lot of the changes to that balance have been aimed at stopping the snowball effect in the mid- to late-game where you don't even have to think about money. You also probably have a higher level of military mobilisation than you did in 2.35, because of the raids and revolt spawns.
Can't change the garrison requirements without making some settlements impossible to hold, it's already at the limits now. You should be spending more on garrisons in 2.35A anyway, so the revolt spawns don't take settlements off you.
They should be both threatening and difficult to deal with if you aren't taking measures to ward them off. If you don't garrison settlements appropriately, the Rebel AI will take them off you with the 8-unit spawns.
The revolts (the 5- and 8-unit spawns) represent local dissent (highlanders who resent the central authority or the like) or cross-border raiding. They replace the hardcoded "bandit" spawns that used to throw out 3 units of Akontistai and pointless stuff like that. They also remind you that no matter how secure you might like to think your hold is on conquered territories, it's not possibe to suppress all dissent and make everyone respect the central authority.
As the Seleukids, you also hold quite a few of the "Troublesome Regions" which spawn those revolts more frequently. And yes, the more territory you hold, the more of them you have to deal with by simple chance. They're random (with a cooldown - so they can't happen turn after turn) but frequent enough that with enough provinces you'll be dealing with them somewhere. Big empire problems.
There's no way to make any of those nuanced changes you suggest without making the whole thing a lot more complex than it is. As soon as you start making things conditional on things like FL Authority, or have them tailored to specific factions, you're talking a lot more code than the present.
Not much has really changed here, besides increasing the maximum treasury AI factions have have from 30k to 50k. We're looking at increasing the cap on the recruitment limitation script for R2 to see if that makes them a little more aggressive.
Also looking to close off the land route between Carthage and Egypt, to stop the "sand wars".