FFXII's plot is a mess, but its a wonderfully written/translated mess. There are some absolutely lovely bits of incidental text that show the writers really cared about what they were doing.
Couple of my favourites: (mild spoilers)
There's an minor npc on Mt. Bur-Omisace watching the chaos following the Arcadian attack and the assassination of the Gran Kilitias who says something along the lines of "I wish it would all burn away, not smoke and sputter so". In context its quite heartbreaking, to me anyway.
Then there's the zen like proverb used to describe the "stack of stones" item. "The world to a child, the weight of the world to an old man". Lovely!
Also have to defend Kazushige Nojima. As a scenarist (plotting, not neccessarily writing) in my opinion he's the absolute best in the world and has been since FF7.
(VERY spoilerish hereafter so beware!)
The perspective shifting involved in revealing the Cloud/Zack duality and the events in Nibelheim (particularly, the "in Cloud's mind" bit) just blew me away back in the day.
FF8 is arguably even better, as it is generally less operatic in its excess and deals with many of the same themes in a more subtle and mature manner.
FFX is brilliantly plotted. Spira its cultures and metaphysics are wonderfully detailed, and its a smart well constructed story to boot. The central conceit (Tidus and the "dream Zanarkand", endlessly summoned by the prayers of the fayth) is worthy of serious literature or film.
I'd also add Kingdom Hearts is quite an achievement too, getting the Mouse House to agree to some of the darker stuff in there whilst binding together all their franchise elements is no mean feat.