I think the spells like Shell, Protect and Bravery combined with the Zodiac Spear probably decreased the challenge of the Sky Fortress somewhat. Obviously if you wanted to make it more challenging you'd remove those. I didn't tend to have any of those automatically set (rather I'd set them as and when I needed them) or the zodiac spear so I imagine it was slightly more challenging for me but I was at a fairly high level when I eventually decided to do it so it wasn't really difficult for me either.