What I could see happening is something that's similar to a Lv. X, but requires a tool card attached to the Pokémon in order to play the Mega. So, you have a Lucario in play, you attach the LucarioNite (or whatever) and once that card is attached, you can evolve into the Mega card.
A few other possibilities, though I don't really care for either of them:
1: Depending on the power of the Mega evolutions in the TCG, the tool cards needed to Mega-evolve (or even the Mega card themselves) may be Ace Specs. I don't really think it's possible, but it does use some existing mechanics, so to speak. Depends on how many cards/mechanics they'll be keeping from the BW series, I guess.
2: Since there's been such a focus on powerful basics, and we've seen a few "basic" stage 2 EXes in EBB (Chandelure, Excadrill), it would be kind of hilariously terrible if all the Pokémon that got Mega-evolutions were in the TCG as basic EX cards and you could only play a Mega card onto the EX.
I really hope neither of those things happens, though. The first because I don't really want to see/play in a format where there's literally one super-powerful Pokémon; it seems like it would make things very luck based. And the second is just funny in a terrible way because I don't think anyone wants to both keep EXes around for that long and also make them even more insanely powerful.
Really, I just hope it's something similar to my first paragraph. It seems like Mega-evolutions would be a great way to put the focus back onto evolved Pokémon rather that another set full of big basics.