My opinion is to add following features to our mod:
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① Forbid vanilla bees to spawn.
② Spawn a random amount of Combees inside wild nests. Rarely, one Vespiquen may spawn inside the wild bee nests. Might need some spawn conditions, too.
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③ Give beehives and bee nests a GUI to help players see what are indide.
④ If a GUI is introduced, u can also let nests become a special ranch which can only breeding Combees.
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⑤ Once players want to get some honey via scissors from nests or beehives without campfire under them, the Combee and Vespiquen would get out of the bee nests and try to battle with players.
⑥ Introduce a way to transfer vanilla honey bottle/comb to Honey item in pokemon. Also add some usage of Honey(pokemon) like attracting pixelmons in ⑦
⑦ Other pixelmons related to bee nests like Beedrill and Forretress would be spawned sometimes if the bee nests are filled with some amount of honey. It seems to be unnecessary to introduce a new kind of tree which have similar function to Honey Tree in pokemon D/P, so let bee nests have this functions is ok.
⑧ It couldn't be better if wild Combees can extend the AI of vanilla Bees.
Of course most of these suggestions are optional, and the implementation of codes seems to be quite tough. Ur guys could think about adding them.
Have seen Mr. SkyTheThunder's comments in https://pixelmonmod.com/viewtopic.php?f=146&t=29103&p=208860 , so hope this system will be interesting