In early 2001, only a few months after the release of Final Fantasy IX, Squaresoft announced their intentions to remake the entire Final Fantasy series on then-current generation systems. I, II, and III were slated for the Wonderswan Color; IV, V, and VI were being planned for the Game Boy Advance; VII, VIII, and IX were to be remade for the PlayStation 2, which came out the previous year. The PS2 remakes would be released on DVDs, with updated graphics and sound, and would also include bonus features. However, Final Fantasy The Spirits Within was released that summer and bombed at the box office, resulting in a massive financial loss for Square of between $50-120 million. The film had been directed by Hironobu Sakaguchi, the creator of Final Fantasy and Square's vice president, who resigned under pressure from company executives. The hand-held FF remakes were delayed for several years (except for the one of III, which was canceled entirely, though it did eventually get one on the Nintendo DS), and the PS2 remakes were canceled entirely.
Final Fantasy II's NES version would have had an English release, but in the end it was canceled as the 16-bit era drew nearer, IV was brought over instead, and II wouldn't see the light of day in the western hemisphere until Final Fantasy Origins. A prototype of the ROM exists, although with a hilariously awful translation.
In the originally planned ending of Final Fantasy VI, Terra would have been a male character in his twenties and died with the other Espers. In the ending of the final version, she receives instructions on how to specifically avoid this fate and does. Recently, lost official preproduction art from Tetsuya Nomura himself has shown up on the internet, and this mystery character shows up in one of the pieces. He heavily resembles Squall.
There was originally going to be a game for the Famicom called Final Fantasy IV. Other than the fact that it existed at some point, not much is known about it except that it was canceled and the Super Famicom/SNES game starring a Dark Knight named Cecil Harvey that was planned to be Final Fantasy V was renamed Final Fantasy IVnote (or Final Fantasy II, in the case of the first English-language version) due to the cancellation of the 8-bit game that was going to have that title. Its cancellation also resulted in every future game having a number lower than it would have had; had the game with Cecil and Kain that ended up as IV stayed as V, we would have ended up with Final Fantasy V being called VI and so on.
The game that ended up as Final Fantasy IV had some portions of its script tossed out before it was finished, not unlike fellow Squaresoft game Secret of Mana. Fortunately, restoring at least part of it was one of the goals of the Nintendo DSremake.
It was always intended that one character would be killed off, right from the very start, and there was also a choice to kill off Aeris or Barret, but they ultimately chose Aeris because she would have more impact than if they used Barret. They were also well aware of the unfortunate implications that would result from doing so.
The game has unused dialogue present in the coding that shows Aeris was going to die a lot later than she was supposed to, but the developers decided to move her Plotline Death to the end of the first disc to induce shock and surprise to the player since it would happen so suddenly.
In fact, Aerith was going to be the only female party member in the game (and there would only be three members, Barret being third). Tifa was added later in development when the writers realized there was no character conflict, and the party would be too flat without something to unify them - in this case, a possible Love Triangle.
Additionally, Red XIII was originally intended to be the character who was cloned by Hojo, as opposed to Sephiroth. After defeating the clones, the party would have confronted the mad scientist and killed him earlier than they do in the actual game. This seems to suggest that Hojo wasn't originally as important to the plot as he eventually became. As for the clones, they were originally going to return as minions of Sephiroth. They were originally named Cobalt and Jade, leading to the idea that they may have been re-envisioned into the WEAPON supermonsters who are minions of The Planet rather than Sephiroth.
Sephiroth himself was definitely no exception to this. Most notably, one of his earliest character concepts was essentially to make him a clone of Kefka Palazzo from the previous game. He was originally supposed to be a man whose Jenova element was awakened artificially due to exposure to Mako energy. His base personality was already extraordinarily cruel and brutal, and had a morbid fascination with destruction and slaughter. Sounds familiar, doesn't it? He also was supposed to suffer from Mako addiction like everyone else, only he becomes much more insane than before, while still keeping his composure.
Sephiroth was also envisioned to be Aeris' brother and then her lover before the writers decided to change the characters to how they are currently.
Jenova is a massive change from its original concept, as explained in "Another Hypothesis". Initially, Jenova was supposed to be a gene that was a part of every person, and that Aeris could use this power naturally because she's a Cetra. Shinra's methods for creating SOLDIER are the same as the final product, but they, along with Sephiroth, were "awakened" beings with the gene. The Turks would be the people who were able to sense the usage of Jenova, and they would bring the subjects back to Shinra for experimentation.
Apparently an earlier idea for Lucrezia was that she was loyal to Vincent, but was drugged and forced to take part in Hojo's Supersoldier experiment. While the actual game has her being willing, the lack of consent probably would have explained quite a few things (namely why she chose to marry Hojo of all people).
Concept Art shows Queen Brahne having a couch-sized cat and Garland would have beared more of a resemblance towards the Garland from Final Fantasy I.
Also, Thorn and Zorn were originally going to be just one character, an old man who was the court wizard.
Final Fantasy X was originally going to offer online elements, but this plan was scrapped early in development.
Final Fantasy XII was supposed to originally have Basch as the main character, as well as a more familiar relationship between Vaan and Ashe (like siblings) which would have given him more of a reason for joining The Party. Penelo's brothers were supposed to be in the resistance, and there would be interactive airship battles ala Star Wars. When all of these ideas were turned down, several developers left Square Enix in the middle of development in protest.
Game director Yasumi Matsuno purportedly suffered a nervous breakdown during development of the game, and left both the project as well as Square Enix. The reins of the game were given to Akitoshi Kawazu.
In a recent interview, Yasumi Matsuno said that it was Balthier who was originally the protagonist, then Basch, and then finally Vaan. This is supported by the fact that Balthier and Fran were the first playable characters to be revealed. It also makes Balthier's meta-references to himself as the "leading man" even more hilarious.
Penelo was also supposed to have a bigger role or at least a more fleshed out backstory. When the idea was presented, the rest of the writers didn't agree with it, so Penelo was reduced to a Tagalong Kid that made sure Vaan stayed out of trouble.
Final Fantasy XIII was planned for the PlayStation 2, the battle system would have been more dynamic and action-based, battles would've taken place on the field map, Lightning would have a much less serious personality and gravity-based powers that influenced gameplay, Serah would have been the seventh party member, and Fang was going to be a male character (explains the Les Yay she and Vanille have, doesn't it?). The entire hoo-hah around XIII and its sequels and spinoffs being categorized into their own subseries stems from the fact that the Fabula Nova Crystallis series was supposed to be a set of Action RP Gs, akin to titles that had recently become popular in western markets such as The Elder Scrolls series and Demon's Souls. Lightning Returns supposedly is a resurrection of this original concept.
The game had a very tortured development period. Early trailers showing the battle system were more akin to concept art, and there was a retrospective consensus that the team lacked a unified vision for how the game would actually play. You can read more about it here.
According to the Final Fantasy XIII Ultimania Omega, the development team at one point considered making Vanille the official main character of the game, but dismissed the idea as they had already released a trailer and art featuring Lightning in that role.
Dissidia: Final Fantasy considered several characters for the lineup, but they were rejected for various reasons. One of these characters was Seifer Almasy, who, in spite of his rivalry with Squall, was replaced with Ultimecia, because he would probably turn out too similar to Squall. Seymour was replaced by Jecht because Tidus and Seymour lacked the kind of personal relationship the other hero/villain combos had. Also included in the list are Kain Highwind,Locke Cole,Yuna, Prishe,Vaan, Balthier, and Lightning, though most of these guys made it into the sequel.
The Ivalice-related spin-off Vagrant Story had a sequel planned for the GameCube sometime before 2003, but it was scrapped.
Having seen the 2012 version of Les Miserables, Tetsuya Nomura was hell bent on turning the highly anticipated Final Fantasy XV (formerly Final Fantasy Versus XIII) into a musical! That's right! A musical! Thankfully, Square-Enix managed to talk him out of it...
Final Fantasy V actually was considered for a North American release as a PC port called Final Fantasy Extreme given that the japanese makers Square thought it would be too hard for the average player and decided against releasing it for the SNES and it actually got under way far enough before getting canned that the PSX version uses the rather bad translation job that was intended for this version as a base for it's script.