>>16935995Quite easily done:
each Pokemon has 6 IVs, which can be between 0 and 31. When a Pokemon is born, it inherits all six from its parents, no matter what, at random, as Destiny Knot almost does now. So a 31/31/31/31/31/31 and a 0/0/0/0/0/0 might produce something like 31/31/0/31/0/31 or 0/0/0/0/31/0/. Then, there are items that make that Pokemon always pass down those two stats. Like an item that locks in Atk and Speed, or HP and SpD, for example. Alternatively, certain items could be given to the daycare lady, or breeding minigames/setups could change, leading to a sort of genetic engineering deal. Like, maybe depending on what items you put in the farm, certain breeding changes would occur.
For a more gamey method that could be cool, you could always just combine Natures and IVs together to make a whole mess of different Natures, that rank the Pokemon's stats from best to worst. So maybe a certain nature might give a 10% boost to Atk, a 5% boost to Speed, a 1% boost to HP, a -1% to Defense, a -5% to Special Defense, and a -10% to Special Defense. Each nature would rank the stats this way, 10/5/1/-1/-5/-10. Or maybe there would be like a nature (10%/-10%), a mini-nature (5%/-5%), and a micro nature (1%/-1%), all either passed down from parents or achieved randomly, depending.