WAIT!
I'VE GOT IT!
For the two natures, we could have two seperate Punett squares. One for the raised stat, and one for the lowered.
So if we had a Quiet/Naughty Vulpix and a Careful/Hasty Ditto...
Raised stat:
stretch +ATK +SPA
+SPD
+SPE
And now for the negative...
stretch -SPD -SPE
-SPA
-DEF
We could use the two outcomes of each of them and that would determine the two natures!
...
Would be kkinda broken though...
... unless you actually want Exadrill with +Atk, +Spe, Sand Rush, AND Sand Force. If that's the case, then computers needs a way to have a hand pop out the cd drive for the sole purpose of slapping.