I like the basic premise of Rahuls theory (his explanation is somewhat "reaching" though) but I feel there is a big gapping hole in it, namely Ellone's involvement in the whole thing, more specifically her obvious acquaintance with Squall from the very beginning (Ellone: Squall...so we meet again.) and her meddling with the team, sending them back in time on numerous occasions through out
disc one which falls in with how the story folds out later on.
Another quote from Ellone suggesting she knew both Squall and Quistis from as far back as childhood: *Squall and Quistis walk into the scene as Ellone is trapped by monsters in the training center*
Ellone said:
Squall!!! Squall! Quisty?
Was Quistis referred to as "whatever her name is spelled in kana"
-chan 
at this moment in the Japanese language version? Which would suggest more than a casual or formal acquaintance... rather Ellone's emotional connection towards Quistis.
A later reference to
Quisty made during Irvine's recollection of life in the orphanage:
Irvine said:
'Cause you two seemed to have forgotten! It just kinda sucked
that I was the only one who remembered... Spunky little Sefie and bossy
little Quisty.
I think the game should be taken at face value, a tale of an introvert breaking out of his shell, accepting the world surrounding him and getting to grips with responsibilities of adulthood facing him, bad as it is in it's execution...
...With short turn around times they had back then I doubt much of the story, other than the general themes and setting got fleshed out before they were already deep in the actual development. Take into account the various ideas on locale, plot events, character development, etc. that (having to fill out 40 to 60 hours of play time) inevitably got tacked on late into development, under time constraints the end result couldn't have been anything but a complete mess of a plot. Standard of major jrpg games' plots back then. I know it's not a popular opinion, but I found FFX much more coherent both in it's plot conception and execution.
Still the game hit at just the right time for me, when I was 17 and could relate to the character of Squall on pretty much every level (embarrassing as it is to admit) and, nostalgia fueled or not, remains one of my all time favorites to this very day...