The Rayquaza thing I already had sort of planned.
Basically when Mewtwo does her Mega scenes, she reveals that Rayquaza gave her the Mega Stones.
I think in canon, didn't Rayquaza EAT its mega stone?
Zygarde breaking into the smaller parts sounds like something she'd do.
Maybe she'll do it too when she lays her eggs, that way each one only has to lay a couple of eggs each!