I have a green male chocobo...

[Aerith's Knight]

Really?

Hmm, then maybe you really could've deleted it. xD

[Skyblade]

The chocobo generator seems to use a very weird RNG. If you load a game, it seems to reset an RNG "list" to a particular point, and the next chocobo that you breed will always be the exact same one (at least, it seems to be that way for me).

But, there is a way to change it. That RNG is used for generating every chocobo. So catch 4, and then save. Breed them (because battles will affect the breeder, eventually). No Blue Female? Reload. Breed again (using the newly reset RNG). Still none?

Reload yet again, and this time, move a chocobo from the pen outside to the stables. This will use up the chocobo generator RNG, giving you a male chocobo with relative stats/max stats of those the green male you keep breeding gets (stats won't be identical due to the fact that the green would be a higher tiered chocobo and receive boosts for that).

Now that that annoying bit of the RNG is gone, breed your chocobos. Didn't get your Blue Female? Reload again, and this time, move 2 chocobos inside (don't save after moving one in, as it will not save the RNG change) and breed again. Then Reload, move 3 in, and then breed for your colored one.

You can also breed one of the ones you bring in with your green male, which will use up another RNG place. You may have to wait before breeding him again, but it will be worth it. So keep this up until you have run out of chocobos, and you should have gotten your Blue Female. If not, go battle and catch more, without saving, and try each time you get a new one.

I've done this alot when breeding for Chocobo stats as well as gender/color.