How about speech bubbles for the villagers similar to Fish Tycoon and Plant Tycoon.

Speech bubbles can show if the villagers is sick, unhappy or even if there is something that they dislike.

I think each Villager should have at least one like and dislike,
it is better then having no like/dislike plus it make each villager more uniqiue.

How about being able to choose where you what to build your huts?
You can break them down and build another in different locations.
This make more jobs for the builders.

How about being able to remove the roof of the huts and peek inside? (Does NOT applies to "Love" Hut)

How about smoke or sparkles appear when your villagers is reseaching, this make the reseachers more intresting to watch.

I think villagers should be able to chat, argue, praise and other actions to all other villager evenly, rather than to just "Alpha Villager"