Let me make one more point that I just thought of. There is a video, that explains exactly what I was proposing:
It was made in 2015. The reason is, because stuff like 100% Dittos weren t supposed to be in the game or lets say - nearly impossible. 100 % Dittos WEREN T in the actual game and NEITHER were they supposed to be in pixelmon . The reason they are is, because Dys introduced manual Ivs editing or nowdays IVs scrolls . In a sense breeding as it is common on this server is highly irregular.
Also: That guy said, he needed to catch around 40 slowpokes to be able to breed a perfect one. I think that is entirely reasonable given how easy it is to obtain pokeballs and how some pokemon spawn in a patch of 5 (another feature original to pixelmon, not the main game)
EDIT: I found a video that explains how it is done in the main game.
There are differences of course, mainly, that she uses pokemon from the same egg group not the same pokemon to get the IVS she desired, but the principle is as I suggested above. You take a pokemon and pair it with a pokemon with the desired IVS until the offspring inherits all the good traits. Again - my suggestion would make breeding actually more akin to breeding in the main game.