Controversial TLDR:
VI is a good game, putting it at the top of the list is just being facetious though. There isn’t a single scene in VI that isn’t executed better or has more depth than those games that follow it from the Golden age (VII-X).
For me the list is ranked in terms of narrative although I still put VII at top just because of the sheer experience of it. Obviously all this is IMO, but you don’t need to be told that:
(Note spoilers for all FF games and Vagrant Story follow.)
VII-VIII
VII is obviously the better game, but I'm ranking them on how well they tell their story. VIII for me works better as a visual narrative than VII. VII has moments of brilliance that outshine the entire series but then there are moments of clumsiness that it down: Biggs and Jesse character models appearing in flashbacks; the insanity of Corel’s (the original town) location.
Dramatically, the show is fine, Sephiroth is a great western villain, although underneath everything his motives are a little primitive. Ultimecia in her final state was a much better villain for me, from her viscous (preferably Japanese dialogue) opening lines to the final 'and...'. VII obviously does more with its playable characters, even the side characters like Yuffie get a major plotline designed to deepen your relationship with the world (Wutai becoming a tourist site).
VIII's use of FMV with in-game action was revolutionary at the time, and I believe I said before, just equip high Junctions (use GF’s boost) and it becomes a visual interactive novel. The storyline itself is touching, and the characters being orphans and knowing each other their entire lives makes sense for when they time travel to the future. The GF storyline and amnesia could have been expanded on more but that's my only crit. VIII's space scenes obviously aren't as meditative and frightening as 2001's Hal arc that inspired them, but I'm sure the 'Rinoa was lost in space forever' scene will be reconsidered as one of the best scenes of the series.
The whole party setup is also why I rank a couple of the other games lower (VI and IX), because the silliness of it gets in the way of the profound. I can accept it in VII, and XIII because the characters are terrorists and need all the help they can get.
X- I rank this fairly high, mainly due to the relationship between Tidus and Jecht, it also has the best ending of the series. It's also the gateway to newcomers of the series, I doubt anyone would try FF7 today (except for enthusiasts) without trying this out first.
IX- Definitely has the best thematic structure of the series. So much so someone wrote a book on it:
http://www.amazon.co.uk/Final-Fantasy-Philosophy-Walkthrough-Blackwell/dp/0470415363. As written in the book, the most explanatory scene was the black mages going with Kuja to extend their lives whilst two stay behind to look after the Chocobo egg. Necron being the main villain makes sense when you consider what the game is trying to say. I actually liked its memory philosophy too, there are definitely real world traits that carry over from parent to child.
VI- Celes’ suicide, the opera house, Serpents trent, Cyan’s family being murdered, the rafting, Shadow’s end… This game is insane, the FLCL of the series, but in terms of art, slow and steady wins the race.
XIII- There is a criticism I’m going to point out in the linearity I don’t think has been touched upon before. There is an attempt here to make stat building or what is now known as ‘farming’ the actual narrative as opposed to an abstract metaphor for the struggles the player faces. Basically the main villain or villains are training their Fal’cie to become strong enough to destroy them. I have seen this done before in Vagrant Story where one of the antagonists is responsible for the presence of monster in order to setup a successor worthy of inheriting his powers, (perhaps others can cite other examples). I really like the Orphan boss and the overall amount of ambition put into the project. The Proud Clad (or is it Clod?) battle was better for me than VII’s rendition.
Major error in plotting: Hope’s mother dying from the same fall Snow has straight after. Obviously it isn’t impossible, but in terms of visual drama it sticks out and screams censorship.
XII- STAR WARS
I enjoyed the Venat and Cid storyline, the fact Cid wasn’t redemptive at all in the face of death, ‘the pleasure was all mine’ makes it better than ‘Return of the Jedi’. Venat’s end was also intelligently done in terms of game plotting, ‘you will not walk this path alone’. Other than that the game is a little dead.
V- I’m putting this above four, purely because of its influence and popularity. My personal thoughts are that I liked Galuf’s world, and all the monsters at EX-death’s castle were pure cheesy fun. Ex-death transforming into a splinter and Gilgamesh are tributes to the ancient stories FF was pioneered on. Faris is an interesting character. I’m tempted to place it higher but I personally didn’t get a lot out of it.
IV- One character is possessed by another who is possessed by another who is- eh. If you ever play Legend of Dragoon you will know this convoluted sense of plotting well. I’ve been told the television series 24 works in this way too. Decent world though, I look forward to playing the remake someday. Most memorable scene? The Dolls and the mutilated parents!!!
III- Never played it. It looks really good though, someone PM me a link since I’m too stupid to find it. It looks more interesting than the two below it though.
II- I sense there is something more to this game, I completed half then watched playthroughs for the rest. I like IX’s rendition of a certain scene in this game, when told back through Ramuh. If a novelisation exists I’ll read it.
I- I guessed the twist before the end. Most memorable scene: The pixel animated brooms.