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 FFXIV 1.0 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.
Urianger Augerelt is voiced by none other than Gideon Fricking Emery, aka Balthier Bunanza. In the 2.0 content, it's not very obvious (because Urianger has so few voiced lines), but once the player hits 2.2 and 2.3 content and Emery is given plenty of material to work with, the resemblance becomes very obvious.
The response to the fatigue system was not very warm to say the least. There may have been aggravating circumstances, but even the developers eventually copped to it being a bad idea to begin with.
The lack of an Auction House (and by extension the existence of the Market Wards) was rather unpopular at launch. When the head of the largest community site for your game goes on a rant about the entire economic system, you have a problem.
The patched in "player history" system during 1.0, which was best described as an ad hoc achievement system and was publicly viewable. While the system itself worked fine, it also promptly exposed a number of stories made by Japanese "official players" playing the game as complete fabrications, as they simply had not done the content.
Ironically, this system would eventually evolve into Realm Reborn's much-better-received Lodestone gateway/armory site.
Lost in Translation: A certain naming issue cropped up when Labyrinth of the Ancients was being added and latter, Syrcus Tower. The Dev Team in Japan, wanting to keep the Crystal Tower dungeons true to Final Fantasy III, wanted to name the final boss of that dungeon after the character it was modeled after, namely, FFIII Titan. Problem is, there's already Titan, the Primal in game. Japan can get around this issue, with a slight change in pronunciation, using タイタン (EN pronunciation: Tie-tun) for Primal Titan, and ティターン (Greek pronunciation, and FFIII spelling: Tea-tahn) for the Labyrinth's final boss. The English, French, and Germany language localization teams aren't so lucky. Solution? Get special permission to rename the final boss to Acheron. Everything was fine, until the 2.3 localization came about, and a certain issue seemed to have slipped the Japanese team minds', the full details of which, are found here, but summed up best with the following.
Fernehalwes, English localization team member: "Fast-forward to a month before patch 2.3. We get a list of the enemies slated to appear in the second leg of the Crystal Tower...and what do we see? アケローン. For those of you who donít read katakana, let me give you a hint: itís Acheron."
The naming issue is also referenced by an NPC within the game, stating that the name of (then) Acheron was mistranslated and has been rectified by the research team.
Lying Creator: Hiromichi Tanaka, reigning champion from his time as producer of Final Fantasy XI, returned 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 was also the case of Guildleves being the main system of gaining Experience Points back in 1.0, but as that comment was made much earlier in development it may have just been an honest change in development priorities. The constant public relations disasters he caused as a result of this sort of behavior (which was much easier to document in 2010, what with a more proactive Internet fanbase and games media) significantly contributed to Tanaka's eventual ouster from the game and even the company.
Word of God: Like FFXI, the 1.0 launch game was very low on the details, such as what your Name Day and Guardian Deity were for. To get concrete info to the public, the community site had 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.
Why The Fandom Cant Have Nice Things: Win trading, the act of giving people guaranteed wins in quests in exchange for gil or items, was very common in the PVP section of the game, which resulted in many people getting high ranks and gear with high stats (including Morale, which is a PVP only stat) without earning them fairly. Frontlines was a second PVP mode added later on to the game and it doesn't use the Morale stat. The act of making Morale useless in Frontlines was very likely done to make sure that people who bribed their way to the top can't have the big advantage over everyone when Frontlines was released. Unfortunately, the motion also punished legit players that earned their gear and ranks for PVP.