It gets too convoluted and self-inflated.
A lot of the game mechanics seem overly contrived.
Aspects of the story that seem to be building up to big revelations (playing as Laguna, Seifer) kind of fizzle. The gunblade is in fact retarded.
All of the characters were too homogeneous; not only were most of them bland, boring, and forgettable, but they were all very similar.
The GF system was too easily manipulated; Junctioning Curaga to HP early in the game = dominance. It is too consciously imitative of FF VII (the name "Squall" is basically the name "Cloud" + bad-assness, SEED just seems too much like a forced parable for SOLDIER).
The story never establishes a clear rhythm; it is wildly uneven and very poorly paced.
Too little "art" and too much "science" went into its design and conception.
Lame, pathetic excuse for an arch-villain (Rinoa parallells aside...even if they were true, that would only add coolness to the CONCEPT of Ultimecia, not her late introduction and shitty character development).
That's why I don't like it as much as the others. I don't hate it, I enjoyed every Final Fantasy. It's just overall kind of meh. Except for the bad-ass, timeless opening movie.
Other people also don't like the uber-sci-fi aspect of it (vs. traditional fantasy), the heavy focus on the romance, and the way enemies levelled up along with you.