You say that you're not sure whether or not to run Tornadus or Thundurus. I'd suggest running Thundurus. The reason why is because Thundurus can be a great starter, and an easy way to get energies into your discard pile. Tornadus is only really ran to counter Donphan, which isn't played very much at all anymore due to 60 damage not being enough to KO really anything. To help get a Thundurus start, I'd suggest changing all of your 40 HP Tynamos to 30 HP Tynamos. The 30 HP Tynamos have free retreat, which can really help with this because since you're running four, if you don't get a Thundurus in your starting hand, you can start with a Tynamo, and then play Pokemon Collector to get a Thundurus and some more Tynamos, drop them, and then retreat it to a Thundurus, attach, and use Charge to get it up and running Turn 2.
Also, you should take out 1 regular Zekrom BW for 1 Mewtwo-EX. If you happen to have your one Mewtwo prized, the game can be much less in your favor, so you want to run 2 which ensures that your going to have atleast 1 non-prized Mewtwo-EX. Also, you don't want to play 3 Zekrom and 2 Zekrom-EX because you're not going to be even using that many attackers throughout the whole game! Heck, the majority of the game, you're going to be either swinging with Zekrom-EX and Mewtwo. I'd suggest taking it out and adding another Pokemon Catcher, which this deck requires you to play 3 of.
With the rest of these changes, you should take out a Super Rod. You are not going to be getting energies out of your discard (since the point of this deck is to get the energies INTO your discard pile), so this card really isn't needed. You're probably worried about what happens if one of your Pokemon gets knocked out. To tell you the truth, you play Eviolite and have a bunch of bulky attackers, so you don't have to worry about that one bit.
From the above, here the changes that I'd reccomend:
-1 Zekrom BW (For another Mewtwo-EX)
-4 40 HP Tynamo (For the Free Retreat 30 HP Tynamo)
-1 Lightning Energy (For Consistency)
-1 Super Rod (For Consistency and Common Sense)
+1 Mewtwo-EX (In case one is prized, plus it's a nice sweeper)
+1 Pokemon Catcher (For Cheap KOs)
+4 30 HP Tynamo (It has free retreat)
+1 Level Ball (To set up Eelektriks faster)
You also might want to take a different, more bulky approach to this deck. The below changes apply to changing your deck to more of a tanking version of this deck than the speed-focused version of it:
-1 Zekrom BW (For an additional Mewtwo-EX)
-1 Lightning Energy (For consistency)
-1 Super Rod (For Consistency and Common Sense)
+2 Eviolite (For tanking)
+1 Level Ball (To set up Eelektriks faster)
As you can see, the above changes don't change Tynamos. This is because that Tynamo has 40 HP, which can survive Kyurem and Tyrogue (which will start being played more due to the recent slow rise in Cleffa's popularity). Also, that specific Tynamo can Paralyze, which is great for stalling so you can set up early game.
In conclusion, I hope that I helped you with your deck, and you'll accept my constructive criticism. I play this deck myself, and I've playtested with it a lot.