What I would have done is allow Silvally to use Z-Crystals to change it's type like Arceus, but if you choose to use the Discs, it raises all of it's (Non-HP) stats significantly (like,
130+ significantly).
Basically, you can choose to have a single super-strong attack, or make Silvally powerful overall; depending on what role you want Silvally to play in your team.
I thought Mega Rayquaza didn't use up your Mega limit, just like Primal Groudon and Kyogre do. Eh.
That team would make for an... interesting Bonus Boss.