User blog comment:Plexioth- xD/Monster Hunter 3 Ultimate/@comment-696610-20130122035420/@comment-1758220-20130122043929

Flagship means it's on the boxart, and most of the advertising. That's kind of the only reason it's considered special. Like, Lagiacrus is the only one that has any sort of in-game significance beyond appaearing in a single low-rank quest (Which Brachy and Narga don't).

Azure Los was featured heavily in the new ad for 3U (Which accompanies the flagship reveal), and will likely be on the posters and other print ads that are released for the game.

I'm pretty sure that the decision to make a particular monster the flagship for the game is made before any story inclusion is figured out, so the latter is basically shoehorned in to make the former more relevant. And, in the case of 3U, Neither Brachy nor Azure Los have anything at all to do with the storyline, as it's still all about Lagi and Ceadeus, so there's really no difference made.