The only advantage I see to the nin over the mnk is the fact he can go straight to the 20% skillspeed bonus, which is useful only when the boss jump a lot. After doing some testing Nin dps is really close to mnk dps, it might look really poweful due to the big numbers but it's actually not that much when you see just how isane is the auto attack damages of a monk over a long fight.

Monk will take advantage when it can keep up GL3, Ninja will take advantage when the boss move around a lot. Pretty balanced, the only thing that will actually make a difference is as always the player's ability to play his job. I'll always take a DRG that know how to play his job over a NIN or MNK that think he is the best dps around when he can barely take the enmity over a SMN.

Game allow you to do every instances with a balanced setup, and that's actually cool.