Your lessons for today: Besides Basic Energy cards, you can only have four of a card in your deck. Second is that Water actually doesn't cover any weaknesses of Fire. Fire is only weak to Water. Water is not any better against Water.
Now for taking out Pokemon. Moltres should be taken out. Reshiram is just a far better basic. We'll take out the Emboar line. It isn't very powerful. A four for 120... Reshiram has a better attack and it's a basic. Plus, Emboar's four retreat cost can trouble you. Finally we'll take out the Blastoise line. Blastoise is an excellent Pokemon, in fact it is one of the best in the game. However, that is only for the specialized Rain Dance deck. Your deck requires Fire Energy far more than Water Energy. Taking out Blastoise will leave more room and allow you to pull off a Stage 2 line that better fits your deck.
Now for cards to add. With the space we have let's add one more Reshiram and two more Kyurem. We have a nice number of basic powerhouses so far, nine actually. Let's make that 11 and let's have those two we add be cards that further support our basic dominance. Lapras has a nice 100 HP and can search for more basics to be put on the bench. Now for a new Stage 2 line to replace Emboar and Blastoise. I'm going to suggest Chandelure whose bench damaging and powerful two for 80 can cause some heavy damage to the opponent. The low energy use also allows you to place more energy on your Reshiram. We'll add two Chandelure, two Lampent and three Litwick. Finally, I'm going to suggest adding two more basics to your deck. Tornadus will provide some handy support for your team, including getting back Energy. That should do it for Pokemon.
For Energy, let's go ten Fire and seven Water. A little heavy on the Energy, I know. But I think it is needed for this deck.
We have 23 spaces available for Trainers. We need to take out an Eviolite, because as of now your deck is against the rules. However, we'll keep the other four, as this deck is very basic heavy. I'm actually going to suggest taking out the three Pokemon Communications. The two Lapras help get out Pokemon quickly enough, so Communication isn't needed. Plus, the room is going to be used for more important Trainers. Let's add another Cheren and two more Catchers. And finally, we'll add four Super Rod to get back Energy lost by Chandelure and Reshiram.
Final Deck: 60
x2 Kyogre EX
x4 Pokemon Catcher
x4 Super Rod
x1 Gold Potion