So as I said, I'm also going to answer. Not that Rio's answer is bad, it's great as always, but just that due to the nature of this deck, there are different paths to take. She's going with low Energy cost, I'm going to go with bench damaging.
So cards to take out. Keldeo isn't the best Water type basic (non-EX I would say Kyurem gets that distinction), so that goes. Tornadus and Druddigon aren't really needed. They aren't the best and they are more at home in decks where you have two weaknesses. Due to the multiple weaknesses of Water, this isn't needed as much. We'll take out the Samurott line, which isn't that great. And that Zoroark line isn't the best. So that also gets taken out.
Okay, so we'll add two of those Darkrai EX. With their bench damaging, high HP, and that free retreat, it will be incredibly helpful. We'll support it with a Kyogre EX. While more than two EX cards can be risky, sometimes risks need to be taken. Three isn't too bad anyways. We'll also add another Kyurem. For a solid Stage 2 evolution line, I'm thinking two Hydreigon, two Zweilous, and three Deino. Hydreigon's bench damaging powers and solid Pokemon in its line help this deck out a lot. Now for some Stage 1s. Two of the amazing Beartic along with three Cubchoo. And two Vullaby and two Mandibuzz. Beartic provides that raw power against the Defending Pokemon. Mandibuzz can either hit hard against the bench or against the Defending Pokemon. With Fighting resistance, it also supports other Dark types.
Now for Energy. I'd suggest 16 Energy. Let's go nine Dark Energy, five Water, and two Double Colorless, which can be put to good use by Beartic, Mandibuzz, Kyurem, and Hydreigon.
Now we have room for 22 Trainers. Let's go three Cilan instead of four. We'll keep the four Skyla you have, as well as the Gold Potion. Then we'll add four Communication, four Cheren, two Super Rod, and four Catchers
Final Deck: 60
x2 Darkrai EX
x1 Kyogre EX
x4 Pokemon Communication
x4 Pokemon Catcher
x2 Super Rod
x1 Gold Potion
x2 Double Colorless Energy