TA2 is just a game without someone to focus it and it shows, the main plot is weak, and largely borrows ideas from the Never Ending Story, in a way I sometimes feel it was written this way as a means to compensate angry fans who thought the first TA game was going to be a simple FF style version of the Never-ending Story and got slapped in the face by the stories heavy subtext. Even the few high points in the game just lack the gut-wrenching qualities of the early works. Its a fun world but it lacks the soul that Matsuno puts into his games and it shows. The man is a master of sleight of hand in his writing and design, always presenting you with something that seems simply only to discover too late the deeper subtext of his work.
I still feel differently about this one. I don't think FFTA2 is weak on themes or ideas, but rather on structure, pacing, and execution.
To me the story always feels rushed and unfinished. The Neukhia is basically completely unexplained, Khamja gets far more development in the side plots than in the main plots, and the main story is filled with huge exposition dumps that don't show up anywhere else in the series.
If the game had taken its time with the story elements, not spent half the main questline with pointless tutorials, and really fleshed out its concepts and themes, I think there would have been a very interesting story there. It certainly has some incredibly strong elements with great potential. But they're almost all discarded at the last minute in some rush to a final boss fight, instead of being explained and getting to come to fruition.
The Neukhia, Khamja, the Whitesilver Magicite, Ilua & Cid's relationship, the relationship between the grimoires, Ilua's relationship to the Chosen... So many things this game brings up, only to cast aside in a last minute scene before the final boss without having a chance to develop them.
And the high points of this game are bloody brilliant. I'll rate Frimelda's storyline above any of the writing in FFT.