Speaking with Eurogamer, Pokémon director Junichi Masuda explained the change in focus, and why Sun and Moon have introduced a new mechanic instead, called Z-Moves.
"This time around we've got various different things for people to enjoy in Pokémon Sun and Moon and one of these things is Z-moves," Masuda said. "This is something every Pokémon can use.
"What we have now is a way for people to use the Pokémon they want to use, so their favourites types, their favourite Pokémon, even those which perhaps weren't so popular before, now they can focus on their favourites in battle. That's why we've focused on the Z-moves this time around."
It's not just about letting you use your favourites, either (as many of the most popular did get Mega Evolutions). It's also a way to resurface little-used creatures and give them a boost.
"Previously, there were Pokémon that weren't perhaps used too much in battle and they're perhaps going to come to the fore a bit more like 'ah, I can use this this way'," Masuda continued, "and perhaps make a different effect than was previously possible."
It sounds like the end for Mega Evolution - at least for now.
"Each time we make a new game, we think of particular theme and of particular elements that would work well with that game," Masuda replied when asked if Mega Evolution might return. "This time we have our Z-moves [but] if a game comes up in future that we think [Mega Evolutions] would work really well with, certainly we'll look into it... But for the minute we don't have any particular plans."
http://www.eurogamer.net/articles/2016-10-19-pokemon-boss-explains-why-sun-and-moon-move-away-from-mega-evolution