You want to be using max potion in here. You can move all the damage to one pokemon (without any energy on it) and just heal a ton of damage, instead of super potion's 60.
The list is looking pretty good. I like the 2-2 Yveltal Sableye split. 3 Darkrai may be a bit much if you plan on attacking with Yveltal EX a lot, so if you find yourself in the need to cut something, think about Darkrai. Other than that, things are looking good.
I've been playing Blastiose with Electrode. That sounds like the cheap way out, but drawing mid turn is actually quite powerful. Beach can still be used, but Electrode has been working pretty well for me.
Pokemon Communication, Trubbish and Pokedex are all out of format. You also have a lot of energy, and you wont need 3 super rod.
-4 Pokedex
-4 Pokemon Communication
-4 Trubbish
-1 Super rod
-3 Grass energy
-1 Fighting Energy
+2 Juniper
+3 Ultra Ball
+2 Heavy Ball
+2 Lunatone
+1...
If you want to attack with round, don't use Meloetta EX, instead, use Exploud. Once you get the exploud out, it's easy to bench more Meloetta, and be able to round for 200 damage.
RE: Cresselia/Mewtwo
Bouffalant doesn't benefit from Gardevior's psychic mirage ability, just in case you weren't aware. I would take 3 Bouffalant out and replace them with 1 Ralts, 1 Gardevior, and 1 Gallade.
RE: Empoleon/Aerodactyl
In my empoleon deck I don't run any juniper. If you can get a few empoleons out, you really don't need any more help. Then you can put Caitlin in the deck, then put in old amber, it just synergizes well.
RE: Mewtwo/Virizion/Lasers
You'll need to take out revive, those are no longer in format. If you want non EX attackers for this deck, go with bouffalant.
The biggest problem is that even if every player had $600 dollars to shell out on 3 beach, there are not enough beach in circulation for that to happen. I think that something needs to be done, because the card is simply not accessible enough.
Is that to prevent enhance hammers or drifblim, or both? If it's hammers you're worried about, you would really only want to attach the DCE the turn it's going to be used. If it's drifblim, then I agree on your call.
You should try running the Drx Durant. It can help you get your resources back. You'd just have to put in a few energy, but that card could help this deck out a lot.
RE: Weezing/Dusknoir
I would take out a bangle and a rare candy; Deoxys will deal with damage problems, and since you only have 2 Dusknoir and you run Dusklops, so 4 is excessive. If not a rare candy, then take out a Dusklops.