I'd like to yet again hint at defining significant movement point differences between captain-led and FM-led armies. Something in the range of 3-4 tiles per turn for captain-led armies and the current base movement for FMs.
It can be done for sure, as Paeninsula Italica II has exactly this kind of script. And while it doesn't completely remove captain-led stacks it seriously lowers the amount of such armies. Oh, and if you are going to implement such, please don't just do it for the AI but for the player as well. It adds a whole new layer of strategy to the game as you simply can't defend your kingdom anymore without a proper FM-led field army - you'll never rush to the defense of an attacked settlement in time if you try to just move out three units without an FM.

(Exceptions would be some densely packed spots like Gaul, southern Greece or south-western Anatolia of course

).