Dueling Games: 1.0 was supposedly rushed out to beat a World of Warcraft expansion to market. This, combined with this game's extremely critical reviews resulted in this approach not turning out well for Square Enix.
The relaunch was coincidentally timed to go along with the release of the final patch of the then-recent WoW expansion, but thanks to the game as a whole being in a better state, it worked out far better.
Executive Meddling: Common consensus is that somewhere along the line, there's been some. The arguments are over just where, ranging from the theory that FF XIV was rushed out to beat a certain popular MMO's next expansion, to claims the developer replacements were an unnecessary move to give executives a scapegoat (or a publicity stunt). The improvements made to the game after the staff replacement suggest more of the former, however.
The patched in "player history" system, which is best described as an ad hoc achievement system and is publicly viewable. While the addition itself works fine, it also promptly exposed a number of stories made by Japanese "official players" playing the game as complete fabrications.
Lying Creator: Hiromichi Tanaka, reigning champion from his time as producer of Final Fantasy XI, returns to (among other things) cause a large part of the controversy surrounding the Anti-Poop Socking system by lying about it being in the game after it was already discovered and hours before it was announced. There's also the case of Guildleves being the main system of gathering Experience Points in the game, but as that comment was made much earlier in development it may have just been an honest change in development priorities.
Word of God: Like FFXI, this game is very low on the details, such as what your Name Day and Guardians are for. To get concrete info to the public, the community site has Q&A topics called Ask The Devs. Since the dev team shakeup, however, there's been much more open lines of communication, although since so much is changing there are often few specifics as to when changes will be coming.