3 Zekrom EX
Pokemon Total = 19
3 Pokemon Collector
2 Junk Arm
1 Super Rod
2-4 Plus Power
Trainer/Supporter Total = 26
Energy Total = 15
For the most part this is your typical Zekrom EX/Eelektrik deck. Hit them hard, discard the energy, reattach it with eel and repeat. Arunnereon adds in dodrio and serperior to make it more of a rogue deck. Serperior heals and dodrio gives free retreat with skyarrow in play.
Serperior isn't going to be effective without reuniclus to move the damage around so you can effectively heal. Healing 60 per turn would make serperior worth keeping. You already play quite a few more supporters rather than collectors, so if you really want to be rogue, and have a chance at making this deck work, I'd add in vileplume. The increased disruption will slow down your opponent, give you access to twins, and will also protect your dodrio from just being catchered. up. I'd drop the serperior for a 3-1-2 vileplume line. I'd drop either the manaphy or cleffa (I'd recommend sticking with cleffa) for another thundurus. This may seem like a bit of bench space, but I picture the ideal with 1 vileplume, 1 dodrio, 2 eel, 1 zekrom and 1 active zekrom (or thundurus until it's KO'd).
With zekrom EX as your main attacker, you want 4 DCE in the deck to ensure that you can hit for 150 each turn without necessarily having to rely on reattaching energy with eel.This deck should be able to work with only 13-14 energy, so I'd decrease your lightning to 10 for now, dropping it further if you find you need the room later.
To get the vileplume up early I'd keep your trainers to 3 candy and 3 communication, and max out your twins to 4. The rest of the deck should be supporters (after keeping your stadiums of course), like 4 collector, 3-4 sage, 2-3 juniper, 1-2 elm, and 2-3 PONT.
The problem that I see with this rogue version is that without vileplume to protect dodrio, it's going to be easily catchered up, destroying your free retreat plan. Serperior's healing ability only effectively works with reuniclus and that's another pokemon that is easy catcher bait. You'll lose a few prizes trying to get up the vileplume, but I'm sure that it'll win more games than the current deck list here.