Why would you purposely build a deck around a negative effect? The "pluses" you described aren't really pluses at all. Cards like Energy Retrieval, Super Rod, and Ho-Oh EX are just fixing the damage you've done to your own deck. They're not helping you get ahead. Also, how are you getting back the trainers you milled? Sorry, but I don't see a deck based around milling yourself working. The one card you mentioned that's good is Eelektrik. Try a more conservative version of a deck based around him. Forget about Rayquaza EX, and focus on solely Electric type attackers, such as Thundurus EP, Zekrom BW, Zekrom EX, Raikou EX, Mewtwo EX, and Tornadus EX. You won't be decking yourself out, and they're just better attackers than Rayquaza EX and Rayquaza regular. Also, Garchomp has two totally different energy costs, so that's a completely different deck, and Giratina EX is basically just a bad card with bad energy requirements.
Rayquaza EX isn't a very good dragon counter, since the most commonly played dragon will be Garchomp, which will one-shot Rayquaza EX for two prizes, while you one-shot them for one prize, except you're wasting way more energies doing so, and you're STILL in a losing prize exchange.
Just as a side note, the regular Rayquaza is almost certainly not coming out in our next set, some thread on PokeGym explains more in depth.