The other Mega Evolution is probably going to be a tough one to predict, though I assume it would be something to tie in with M. Rayquaza. My guesses are:
M. Ampharos-EX - The reason being is because Ampharos was a version-exclusive to Emerald, but I could always be proven wrong.
M. Blaziken-EX - Blaziken so far hasn't gotten any Ancient Trait cards. (considering how popular he is, one for him would have been leaked by now) The Pokemon company is definitely building up for a big Blaziken reveal, so this is probably the most obvious choice.
M. Gyarados-EX - Gyarados is a Pokemon that always has felt like a Dragon Type, and considering how much of a Fanbase he has, I think it would be a healthy addition.
M. Salamence-EX - I doubt 2 Dragon Type Megas would be in the same set, but there's always the possibility! Salamence is a Pseudo-Legend, anyway!