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Mega Metagross, for sure.
I figure a lot of the reasoning behind giving certain Pokemon Mega Evolutions is based on things arbitrary to the games themselves, like popularity (as evidenced by many of the choices). If this is the case, then now is the best time to debut a Mega form for Metagross.
It was one the dual pseudo-legendary 'mons in Gen 3, has a distinct look, is well-known enough to appear in Smash Bros., and is the main Pokemon used by the champion in the upcoming remakes. If they're ever going to make Mega Metagross, now is the best time.