They don't clash at all when you remember that the games are designed with VGC in mind competitively, which means that Item Clause is a thing. If anything, it's quite complementary to Mega Pokemon - if one Pokemon on your team has a mega stone, and one has a Z move stone, that's fewer Pokemon you're trying to scrape the bottom of the barrel for when choosing items.That's it, I can't see new Megas appearing this gen. Not the concept being scrapped, but I don't think we are getting more, given how the two concepts clash.