Quote Originally Posted by Cairdeas View Post
They didn't have a working Crystal Tools build until about 2 and a half years ago though.
http://ps3.ign.com/articles/702/702289p1.html
Speaking with Impress Watch on the eve of the Final Fantasy XI: Treasures of Aht Urhgan launch in Japan, FFXI producer Hiromichi Tanaka stated, "As we work on Final Fantasy XI, we're currently working on a new MMORPG targeting Windows Vista and PS3." Square Enix is hoping to make the game a worldwide title, Tanaka added.
"Working on" means "working on". They were working on it as late as 2006.

Furthermore..

They said they don't have Chocobos because their anima system covered transportation and they needed something else for Chocobos to do.

You don't need a game engine to at least think and plan for something else for Chocobos to do.