Please, please someone make a Charizard/Emboar/Vileplume deck so someone can say they've dealt 1200 damage. lololololololol
Both these cards are pretty bad. As Blah said, they're useless in Emboar because Rayquaza can already do 300 damage. The Mega effect just isn't worth keeping the Energy and not having to play Lightning Energy. They might be funny to play with Aromatisse to just win in 3 turns after getting it out, but Charizard/Emboar is just pointless.
Y is slightly better than X, because the drawback is better, and it only has 1 retreat, as opposed to X's 3, but X does have more HP and a better weakness (and don't say Black Kyurem, because Y is weak to Keldeo, which is worse). I was going to say that with X, you could play Darkrai to give it and the rest of your deck free retreat, but you can do that with Y anyway.
Protect Cube is pretty solid. It's definitely worth it in decks that deal damage to themselves, but I don't think it will make those deck more playable then they are currently.