Sometimes you will want to retire your chocobo early. Here's why (and I'm speaking from the experience of having a Rank 9 damn near perfect bird) --

When you breed upper level chocobos in your quest to get a better pedigree, there are many points that are somewhat RNG involved. Your new bird inherits a trait from either the mother or father, plus some of their stars in the major categories (speed, endurance, etc). The only way to know how many stars YOUR NEW chocobo got is to register it with the Chocobo racing registrar at the Gold Saucer.

And then let's say you got four stars in everything but stamina and cunning, and those are just one star. Not very good, and you don't want to spend the time and MGP to level up a bird's rank that's not going to perform in the race for you. So you retire it then without wasting time, and it becomes chocobo nuggets for the Gold Saucer cafe

But you still have 9 more opportunities to breed your retired rank 40+ chocobo, so 9 more chances to see if you get better star ratings. You can see "sort of" what the outcome will be when you purchase the covering permit for the opposite chocobo sex from the Tack and Feed seller. You can see the star ratings of the Sire/Dame, and just discard the ones that aren't very good. Yes this costs MGP. But you should be able to get it back as you increase in rank and reach higher tier races.

Clear as mud?