There are really gaping problems with the one world theory, though many of them can be resolved by getting very creative.
You know, things like:
After FFVI,
(SPOILER)all magic is gone from the world. Not to mention the damage Kefka managed to do to it- Sepiroth *almost* crashed a meteor into the world, but Kefka re-arranged all the continents, and turned a sea-trench into an island. This suggests that FFVI should probably come last.
The early games are heavily dependent on crystals. Usually elemental crystals which vary in number. Destruction of these tends to do things like bring about the end of existence. The later games do not suffer from this at all.
FF IX had many airships, but most ran off mist. All other airships do not need mist. By the end of IX, there were many ships which did not require mist. Howver, IX had summons, and early ones did not. (I am tempted to ignore this part however...)
It's fun to compare. Any list I make starts off with IX- airships advance, a single crystal is shattered by Kuja, who perhaps also created/summoned the four fiends. The shattered crystal could arguably become the many elemental crystals of the later games. Black Mages are created in this game, so any game featuring them must come after IX. (perhaps they are not created after a point).
The list also always ends with VI. Magic has ended at the end of the game. The world starts off recovering from a near-apocalypse with destroyed much technology, but some still exists. Also, Kefka does such an insane amount of damage to the planet before he is stopped. Most villans don't manage to do quite as much.
Other associations: IV and VIII may be at least relatively close to one another, due to the moon being covered in monsters. However, the crystal era must end sometime between them.
VII must come late enough to be post-crystals. I feel it arguably comes after VIII, but it can go both ways. (Estar -> Midgar? The increase in gun-like weapons supports this. However, the greater freedom of space travel in VIII does not. Probably, need another FF in between, perhaps one not yet created.)
FFI could come very early on. Not only is there a strong link between I and IX with the crystals and fiends, but the airship in I could be lost technology from IX.
Really though, I think they are entirely seperate. It is fun to compare however.