Instead of any two bees being able to breed when "fed" a flower, there should instead be Queen bees who are fed nectar (or honey) by their bees when they enter the hive. The queen bee is slightly larger than a normal bee (which should be smaller than it is) and slightly darker in colour.
When fed enough, the Queen Bee would check how many bees there are within a certain radius (however many blocks from their nest bees can wander) and if there are less than 10 (or a lower number, just spitballing) she would create a new bee.
The queen bee spends most of her time in the hive, however if it's destroyed, it leaves and tries to find another one (possibly having other bees attack the player?)
This would not only make bees more realistic, it would also make their breeding more unique and interesting than the standard fare of just feeding two of them.
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