Agreed. When Galuf died (Press F), his skill points were transferred to Krile. Conversely, any EXP you've sunk into Aerith is just gone. And since she's a dedicated healer, odds were Aerith is in your party a lot. I can't emphasize how subversive that was. Even today, it just isn't done.
As for the shippers: I have always considered them a cancer, not just in 7 but in entertainment as a whole. Really, can they stop playing with themselves while watching slow-motion Clerith GIFs for two seconds and just watch for the story?
Cancer metastasizes. Once the writers pay attention to this specific type of fandom, they tend to derail the plot to focus on the shipping.