I was thinking maybe each village's forest should have enemies that would make sense for that village.
i.e.- You encounter Sound shinobi (Tayuya) in Otogakure, and Leaf Shinobi (Rock Lee) in Konohagakure.
I can see there not being enough village specific enemies for each forest but there are lots of generic encounters (most of the lower level monsters) to fill the gaps.
Another idea would be to just increase the likelihood of encountering a village's own in their forest, because a resident of Konohagakure being in Kirigakure isn't unheard of etc..
Missing Nin, residents of uninhabitable villages, random monsters, etc. would not be affected.
I haven't been active on the forum for a couple years but I did a quick search and couldn't find anything similiar, so forgive me if I'm mistaken. Thank you.