Pokémon Omega Ruby and Pokémon Alpha Sapphire announced

Really hoping they kept trainer customization, but won't be too surprised if they don't.

It's important to remember that the reason some features disappear between games is because Gamefreak has two teams.

The pomegranate team who make remakes (including third versions such as Emerald or B/W2) and the mainteam who actually gets to make the new games. Even if it goes away this game, I suspect it'll be back for the one after.

As a nod to your trainer in X or Y being given a Kanto starter to run the same task? Yeah.

But if you're talking about the actual first mega evolution, it's heavily implied (if not directly stated) that a Lucario led to the first mega evolution.

I wouldn't try fitting a timeline to pokemon. The R/S/E games are supposed to take place at around the same time as Red and Blue, so this would be retconned to the place where mega evolution is discovered.