RE: Eelz/Empoleon
In BW-on, any good deck needs 4 Junipers and 4 N since they are the only decent draw supporters (well there's Bianca, too, but it's not as good since it doesn't always work).
Currently, your supporter line looks like:
2x N
2x Random Receiver
4x Bianca
A good supporter line in the BW-on format looks like:
4x N
4x Professor Juniper
2x Bianca
2+ Random Receiver
Professor Juniper is good because it gets energies in the discard faster for you to Dynamotor. If you have some valuable cards in your hand such as Catcher when you have a Juniper, luckily you can either play N or Bianca instead (or just Random Receiver and hope for the best). This might seem a little risky, but it's much better than the supporter line you have. This is because with so little supporters, you could get into a supporter drought, which could possibly lose you the game. Heck, for a while I was testing with 4 Junipers, 4 N's, and 3 Random Receivers in my Eels list and even then I would run into supporter droughts. This line would prevent you from not having one in your hand, thus making your deck a lot more consistent. In order to spice up your supporter line, I would do:
-2 Empoleon
-2 Bianca
-2 Prinplup
+2 N
+4 Professor Juniper
Right now, I'm starting to take out the Empoleon line. It doesn't fit very well into an Eels list, and Empoleon is a completely different deck. If you still don't agree with me and decide to run it, then make sure to play more Max Potions, since Empoleon's attack only costs one energy which means that you can just attach another and continue to steamroll.
Continuing on with your list, I see you only play 3 Catchers. Remember that since there is no Junk Arm in BW-on, that 4 Catchers is a must (unless of course, you're playing a Darkrai varient, in which case you can play 3 because of Sableye). Also, Pokemon Communication isn't needed anymore since we are getting rid of the Empoleon line, and you can use that space to add additional Ultra Balls which will make your deck even more consistent than Comms would.. Ultra Ball is a great card in Eels because it is the safest way to get energies in the discard so you can Dynamotor them back up. A cool thing to do with Ultra Ball is play it to get another Eel, so you can Dynamotor the energies back immediately. From these explanations I'd make these changes:
-3 Pokemon Communication (see above)
-3 Rare Candy (Not needed anymore because Empoleon is out)
-2 Piplup (getting rid of the rest of the Empoleon line)
-1 Energy Search (I played Eels/Terrakion at Nationals and had no energy drought)
+1 Pokemon Catcher (Remember, no Junk Arm, so 4 is a must)
+1 Eviolite (See next paragraph)
+2 Ultra Ball (To get lightnings discarded faster and a quicker set up)
+1 Switch (Can really help if they Catcher up your Eels, which they will do)
+1 Max Potion (Great for healing Zekroms in coordination with Switch)
+3 Plus Power (Allows non-ex Zekroms (which we will add) to OHKO Terrakions and Terrakion to OHKO Eviolited Darkrai)
Now, the main strategy of main Zekrom Eelektrik lists is to go aggro Eviolited Zekrom most of the time to 2HKO anything in the game. I saw you didn't play any Zekroms at all and only one Eviolite. Since your choice is Zekrom-EX and you only play one Eviolite, that leaves you very vulnerable to Terrakion OHKOs. For this reason, I'd suggest playing less Zekrom-EX's and more Zekroms- Zekrom BW is better because of both of its attacks, its ability to abuse eviolite, and it only gives up one prize.
Continuing on with your Pokemon lines, I'd suggest taking out one Eelektrik (since you play 2 Super Rods). Also, take out one Eelektross, since it's really not needed in a format without Vileplume. In the place of those, I'd suggest adding in 2 Mewtwo-EX's. Mewtwo-EX is a great surprise late-game sweeper, and it can also win you Mewtwo wars (yes, Mewtwo is still going to be played in the BW-on format, believe it or not, thanks to it winning nationals). It's ability to power up with every Dynamotor is awesome, and it can easily 2HKO anything. If you play Mewtwo, just make sure not to drop it in the Darkrai/Hydra matchup because then they will either 2HKO you with Darkrai, or bring up Sigilyph and hit you for weakness. Finally, take out one Thundurus and add one Terrakion. This way, you can make sure to hit revenge kills more easily. In the approach I'm taking, you are going to want to start with Zekrom instead of Thundurus. This way, you can take damage to start powering up an Outrage.
From both of the above paragraphs, here are the changes I'd make:
-1 Eelektrik
-1 Eelektross
-2 Zekrom-EX
-1 Thundurus
+2 Mewtwo-EX
+2 Zekrom
+1 Terrakion
Also, you're going to want to take out 2 water energies and add 2 fighting energies since you don't play Empoleon anymore. This is also good so that you can hit Retaliates more on Terrakion.
From every change I've made in this post, your finalized deck should look like:
4-3 Eelektrik
2 Zekrom BW
2 Mewtwo-EX
2 Terrakion NV
3 Switch
2 Eviolite
3 Ultra Ball
2 Max Potion
3 PlusPower
4 Pokemon Catcher
2 Super Rod
4 Level Ball
4 N
4 Professor Juniper
2 Bianca
2 Random Receiver
8 Lightning Energy
4 Fighting Energy
Hope I helped! :]