Both of these races consider all other races inferior, and themselves the best. Why are Gityankas better than mind flayers? Why do they have a conflict if they are so similar?
Because their ancestors were enslaved by the illithids for countless generations. It seems to me that this is not conducive to the union.
It's funny, githyanki don't like to hear a lot of ugly things about their race, mostly because they're all true. The first and foremost is that they're a bunch of hypocrites; obsessed with "being free" that they have become convinced their manifest destiny is to conquer & enslave every other race in the multiverse, and they hate religion but worship the Warrior-Queen.