I have a suggestion for advanced beekeeping. I posted this in Discord in condensed form but thought it would be good to put it here as well and elaborate on some ideas.
If I could mod I'd make this myself but, alas, I possess no such skill. Besides, I think this would fit great into the base game.
Currently, the only way to get honeycombs requires the player to entirely destroy a bee colony. And with the addition of seasons in the future, it would keep with the realistic theme of the game if bees in skeps died in the winter and would have to be re-collected from newly spawned hives in the spring.
Therefore, I suggest a later-game multi-block apiary that functions more similarly to modern RL apiaries, with wooden frames in which the bees build their honeycombs.
The player would have to take out the frames, scrape off the honeycombs (possibly even manually, like with smithing and knapping), and then process them as we do now.
With such an apiary we could ensure the survival of our colonies during the winter.
Gameplay balance ideas (and suggestions for seasons):
The frames would be destroyed in the honeycomb-harvesting process so new ones would have to be made to replace them after each harvest. If they're not replaced in time (within an in-game day?), the colony will despawn and the apiary will be empty again.
Because the swarm can grow larger in the multi-block apiary, the player would first have to smoke the hive with a smoker (crafted with metal plates, fuelled with dry grass and has to be ignited before use) in order to safely remove the frames from the apiary. There would still be a chance (though much lower than for skeps) for an angry bee swarm to spawn, in which case the player would have to wait to harvest the frames until the swarm has despawned, or face the wrath of the bees while he works to take out the frames.
A colony in a big apiary would take a bit longer to grow and mature after swarming, and take longer to replenish the honeycombs after harvesting, but they'd yield significantly more honeycombs than skep colonies.
Realistically, bees mainly swarm in late spring and early summer, with occasional smaller swarms at other times (except winter). For the game I suggest that colonies in big apiaries swarm more rarely than those in skep colonies (maybe even only once a year?), but both only in late spring - fall. This way, skep colonies can be used to grow the number of bee colonies and wooden apiaries can be used to have a bigger, more regular yield of honeycombs.
To survive the winter, colonies in big apiaries have to be manually supplied with a small amount of honey, or one frame of honeycombs has to be left behind during the last harvest.
Now on to the building of apiaries. I suggest that an apiary requires two unique blocks, one main one which holds the frames and another one in front of it that acts both as the opening for the bees and as a door for taking out the frames for harvesting. To make this a somewhat later-game structure, on top of using boards to make it, it might require crafting metal hinges or something. The frames could require string to craft.
It could look something like this (with more colour variation )
When the frames are ready to be harvested, the player can open up the front part like a door and take the individual frames out by aiming and right clicking, and put new ones in the same way.
The remaining five block faces of the main block would have to be covered by any wooden or brick blocks the player wants to use. They could be chiselled as long as the block face connecting to the main apiary one is completely covered. This way players can design their own apiaries.
Really simple designs.
Put multiple apiaries together.
Or build some creative ones!