This is just one of the ways the game shows an aspect of real life. Wakka was brought up to hate the Al Bhed and thus he did, without even knowing much about them. They were simply 'bad' to him. But when he finds out Rikku is an Al Bhed he starts to realise that maybe behind their masks, the Al Bhed are really good people, just like Wakka himself.

As for SW, Jango and young Boba were New Zelanders lol, I don't see much racism there, besides Jango was by far the coolest character in Ep 2, I even have a figurine of him