Genetics - Color Heritage
It is my belief that Genetics or Color Heritage is the key to successful breeding based on color. I'd say the majority of chocobo raisers, breed with the main intention of achieving a certain color.  Everything else, comes in second, and I say this because no matter what color your bo is, you can still mold it to be a Racer or a Digger.  So pre-establishing its color from the start is important regardless what its agenda is.

Other techniques for Breeding besides Genetic Breeding include:
1. Ability Breeding: Breeding with the intention to inherit a certain ability.
2. Stat Breeding: Breeding 2 Chocobos maxed out in a certain stat, combined with the equivalent Honeymoon packaging giving the Chocobo an initial minor boost with that stat.
*** However, first-time breeders should realize that abilities can be learnt while raising and the initial stat boost is not significant.  While color inheritance can be tricky if you don't know what you are doing.  Plus, there's always an element of risk involved meaning color is never guaranteed 100%.

Speculation versus Fact:
It's virtually impossible to "prove" color inheritance is based on Genetics. One would need to raise a hundred+ Chocobos and follow the exact same food and agenda for Chocobos derived from the same cards. In addition, the same scenario would have to be enacted using the exact same egg-type, bought from the Jeuno NPC perhaps.  Such a test is unreasonable and, therefore, Color Inheritance remains unproven.

I'd like to state that I may not be the absolute source in Chocobo Raising, but I've raised 18 Bo's and served my time.  I keep careful track of each Chocobo's genetic history (every Chocobo has its own family tree written out) and have reached 8th Generation without interbreeding at all, ensuring the Family Trees are not confusing.

My personal ranch of 18 Chocobos has been very successful with achieving the colors I've wanted, using Genetic Breeding.
The cards I sell are from Chocobos with a strong Color heritage which I've genetically engineered to greatly increase the chances of successfully achieving a desired color.
I've sold and given hundreds of cards out with a very high color success rate.  I have spoken directly and continue to speak to my customers on numerous occasions, acquiring feedback and the vast majority acquired their desired color following my Genetic Breeding advice.

My personal experience proves to me without a doubt that the major key behind successful color breeding is breeding Chocobos with a strong color lineage.
 

Breeding Guidelines:
1.  2 Colored Parent Cards:
It's key to start off with 2 cards of the same color.  Breeding 2 different colors severely drops the chances of acquiring one defined color.
Everything beyond this principle greatly increases your chances of acquiring a defined color.

2.  Know the Genetic History
Obtain a card from a Breeder that keeps track of their Chocobo History.  If the owner doesn't know their Chocobo's history and information, you won't know what your chances are of acquiring a defined color.  The likelihood that you'll acquire incorrect information about their Chocobo's stats and abilities is also great.

3.  Blink out the Yellow!
a)   Do not obtain cards from people who cross-bred using a Yellow Card.
For instance, if you want a Black chocobo, do not obtain a card from someone who bred a Black with a Yellow.  This lowers the Black genetic strain.
Also, because yellow is a Chocobo's "default color", that probably makes Yellow also Dominant over Black.
Following Principle 3a. and 1:
b)  Do not breed a Colored Card with a Yellow!

4..  Generation Gaps
This guideline is very important, and although is a reiteration of previous guidelines, is still a separate principle.
 
a)  Look for Chocobos 3+ generations.  This gives a solid family history right off, and ties in with Guidelines 1 and 2.
 
Breeding a 3+ Generation Chocobo with a 1st is also permissable since it's the 3+ Gen Chocobo that builds the genetic foundation in this case.
b)  If Recent generations (namely the last 2 generations  (parent and grandparent) are uniform in color, that greatly aids in inheriting a defined color.  Parent and Grandparent genes do affect the new Chocobo's coloring.
As stated in Guideline 1, the Parent cards' colors are the most important in defining the color of your Chocobo.
 
From personal experience and accounts from others, color variation appearing in a Chocobo's second and third generations influence the genetic outcome of the new Chocobo.
c)  The more Generations the Chocobo has of unified color, the stronger that Chocobo's color strain is.  Although generations past a certain point would not affect your Chocobo's color, they have certainly affected the more recent generations colors, which in turn affect your Chocobo's color.
Plus, it really is nice to raise a Chocobo with a history behind it.