Well you kind of answered your own question. The Den of Woe felt so grim because the majority of the game was very light-hearted. Therefore X-2 cannot be "the darkest entry."

Also this whole thing is rather subjective but XII never felt that "dark." For one thing, you were never out to save the world in the most conventional sense. Sure, Archadia was bad but compared to the antagonists in the other games, they are almost saints.

Worst case scenario for XII is Vayne conquers the world. Oppression of non-Humes, dictatorship, etc.

\Worst case scenario for X is that Seymour kills everyone or Sin keeps on killing for eternity.

The situation was much more bleak in Spira.