i've heard that if you breed 2 grey ponies in V2(both with grey mane, grey body and grey eyes) the foal may be all black, or withe or have like... withe mane, grey body and black eyes or something like that...
i think the new system makes the baby pony's color be a variant to the parent's color...
for people who like to have ponies of several different colors, and uses to get new ponies throug breeding, this is good, because the pony may not be the same color as his/her parents and they'll not need to look for glitches nor ponies of a radicaly different colors than the mother to get some variety.
however, for people who like having all ponies of the same color(or close to it), this is very annoying, because they are no longer sure the baby will be the color they want it to be...
if you'd like to take a look at my ponies and ask questions about their ancestry, i remember most of their parents.