Even so, it's sad that something as fundamentally Final Fantasy as chocobos not being in a NUMBERED FF game is being defended by anyone. Not even SE should be able to defend this.
Hate to break this to you but FFXI didn't have chocobo's for the first 4-5 months in JP Beta. Now should SE have learned in the 10 years since XI has been out? Probably. But don't go around acting like they owe you something just because the name "Final Fantasy" is on it.