Well I'd just like to point out some things:

Yes the Berserker class changed, but I really really loved it. Think about it, you have the berserk ability at least, and the costumes are barbaric almost, giving that primal instinct sort of look, which would cover the Geomancer theme to some degree.

And about the ninja class, yes it seems to be a classic job BUT, they covered that quite nicely with the Berserker. How? Well, each girl has their own unique fighting style.

Yuna: Acts like an animal in a pouncing position. This style can be related to lots of traditial Martial Art styles, based around the tiger and other cat-like animals.

Rikku: Oh comon ain't it obvious?? It's Capioera! Probably my favorite type of martial arts. It's a Brazilian style of fighting/dancing. Eddy Gordo and Christie Montiero use this style in the Tekken games.

Paine: From what I can tell, her style is that of boxing/kickboxing.

Dragoon would have been nice...
And I thought the Gun Mage was a variant of a Red Mage? ...I dunno