I haven't try this solution, but try to play the game without the Abandoned Thand and without Zora until you enter the FreeGate. I don't know if they are going to join you later if you ask them. I'll begin a new game and I'll let you know (unless you find out before me).
I have reached the Shaper Crypt but I can't find a way to open that stone gate. A text appearing asks me to put something on the glowing runes... Does anyone knows what this "something" is (and perhaps where I can find it)? Thank you