Im having the same problem sorta.
People and guides say that if you give a everstone to the female be it the actuall pokemon or the ditto it has a much higher chance of becomming that nature. and yes i belive that to a point because after a year of breeding and making diff teams iv seen it happen.
Altho one thing i have noticed that is that this ditto that i have which is a Serius one whome IV's are near perfect all 29+ and 2 31 IV's in Atk special Def never seems to breed correctly with the other pokemon im using.
For example I breed with him with say a female snover thats sassy holding a everstone. After 3 days of breeding and a near blisterd thumb i only got 2 sassy snovers, the rest were all random nature's.
Now most people always laugh at this saying "even with a stone its not garunteed" no kidding genius's. But i decited to breed the snover with another one that had similer IV's but not as good to my ditto and i got tons of sassy ones after an hour or some about 9 or so.
This happend to me on my entire team the ditto will not breed with a female pokemon holding a everstone and get that nature that the female has. Its only works when they breed with there own species so i have to breed tonso f pokemon until i get a male with similer IV's to the ditto to start getting the good sassy ones with the female.
I belive it does this with other ditto's i have to but i forgot cuss i dont use them anymore. It might be because this ditto a neutral nature im not sure. All i know is this "everstone on a female thing" doesnt work with ditto's. The ditto's seems to pass there nature on for the most part, but paring the ditto with a female holding a everstone it never works.
There is more to breeding then meet's the eye. Same with natures being random i dont belive it. I think natures have percentages. Iv noticed while breeding normally that i always get Naive, Lax, Relaxed, hardy, bashfull, mild, serious, naughty, quiet, docile alot. Serious, relaxed, Docile, and Hardy more often then other's. Adament, Jolly, carefull,timid, Bold, sassy, gentle, carefull i hardly ever see.
The rarest seem to be Adament, Timid, Jolly, and Bold.
This cant be random cuss it doesnt explain me getting repeatedly same results after a year breeding on this game. I bet its based on percentages like i mention and the natures that arent very good are more common then the good ones.
I dont care if no one belives me, but im mearly stating what i have observed