In my Macedon campaign I've conquered nearly all of Greece at this point but it struck me that I never once saw an enemy unit lead by one of their generals. The generals exist, obviously, some of the more important cities are full of them, but they do nothing except sit in their city until it's conquered. Why aren't they out in the field, leading their troops?

Why aren't they out in the field, leading their troops

- Sometimes they do (e.g. Illyrians).

I agree, it seems like an easy addition for the AI to attach a general to a unit on deployment if on is available.

Yes, it seems like such a minor fix that I'm wondering what reason there could be for not letting enemy generals lead units.

Aha - I checked for anything like this a month ago and no one else had posted anything else. I am now continuing my campaign and it was brought to my attention when capturing a city state in Thebes area it had around 10 generals.

I have no idea, but can it have something to do with the difficulty-level? I mean the generals do add abilities to the troops and at lower difficulties it might make sense to leave the generals out of the game while at harder levels they will be part?

Difficulty level has nothing to do with it. Hegemony lets you customize a lot of game settings to tweak the game experience but enemy generals is not one of them.