Yeah Sylon is right, I believe the only way around this is changing the strength 'strong' & 'weak' equations which in turn change the algorithm that controls army assignment. To explain the armies (or any unit) which gets moved into a fleet are viewed as insanely strong which is probably in effort to make the AI sink the ships.Two issues I've noticed:
Firstly, CAI tends to ignore undefended settlements (major and minor). Its behaviour is much more logical if they are garrisoned.
Secondly, there's this ford that can't be used since one of its banks is mountains:
I'm not sure if it's meant to be usable or not, but I think either there shouldn't be a ford or both banks should be passable.
However, when there are absolutely no armies in a town, I suspect that the town is viewed the same way because there is no assigned strength to it but yet it's an enemy objective the default value for such an up in the air target may also be insanely high. As such, the only way I've ever seen the AI regularly take such a town is a) if it's a part of their victory conditions and b) if the str limit is at 999 (effectively disabled or insanely high enough that the AI tries to take the town). The major downside with that, is that it induces chaotic behaviour in other areas, for example field battles, sieges and naval battles with all often be lopsided in your favour without the limiting factor of the highest strength army the AI can engage.
There are many other factors as well that come into play where the LTGD is involved, nevertheless changing the str limit is definitely something I don't want to do after tests and recent reports about how the AI is behaving with a new more 'astute' value which aims to have the ratio be 1:1 when engaging.
edit:
I forgot to mention in vanilla it was a value of 99, probably contributing towards the random once in awhile 'suicidal' attacks. However, it may have also played a role in AI behaviour towards empty towns fixing that bug. I however, find that in EBII towns almost always have a garrison as without one your public order will be nearing revolt or at a revolt level. Therefore changing the value isn't a necessity, unless of course you find differently... I haven't read many, if any, reports about that part of the game. (how the player garrisons their city)
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