Maybe you only start out with essence seeds and you go into different branches of progression, so, for example, you could mutate an essence seed to a metalic seed and from there you could morph it into other metal seeds, like iron.
Sounds to much like bees. Bees are to end game. Unless your name is Jaded.
And I hate that many of the bees are useless except for getting other bees. It's a waist. It would be better if it were used to modify and eventually improve the resource generation.
Basically as a default normal magical crops would only have a chance (25%ish) of dropping a nugget and it would take a while for it to grow and be immune to being speed up. And through breading you could get up to 3-5 (veriable) ingots a plant, be much faster, and able to speed it up. Maybe even letting normal bone meal work on it.
From under to over power depending on how much time you spend on developing it.
You could even used ore berry bushes as a source of the initial seeds.