Okay, this time at work again (I'll never learn I guess? xD), but I'm having my break, so I'll see what I can put up for you. I'm commenting on your updated post though! Let's take a look!
Pokémon
Okay, after reading your posts, I can see where you are going with the Thundurus + Twins. My own testing (and preference) has shown me that with 4 Juniper, 3 Sage, and 4 Junk Arm I have no problems with getting my energy in the discard pile. While I'm getting to this later, I think I should also mention to you I even run one less energy than you (ie, 9 Electric and 4 DCE). Once again, I'll get back to that later, don't worry. All I can say is that you should play what you feels that plays the best. A word of personal advice though; While your ''Twins setup plan'' might work, keep in mind that you're sacrificing a prize to do so. In this aggressive format, giving away free prizes isn't such a good thing unless it gives you the ''push'' to make it a game sealer (ie, you can get everything you need to win the game with that Twins you use). I doubt Twins gives you this, but once again, it's personal preference. My own experience that is with enough copies of every card, along with enough consistency cards, you should never really need to search out anything, as with Sage and Juniper you should often get everything you need. Try it for yourself and see whats takes your fancy.
The reason for the 30 HP Tynamo is short and simple (and you said it yourself already); It has free retreat. This can not only be useful early game (when you don't already have Eelektrik going), but also late game when you need to promote something in response to a KO, but still need to Dynamotor something before it's ready to take action. You can now free retreat, with minimal resources used. Of course the 30 HP is horrible, but 40 isn't much better either. And if you don't feel like needing a free retreater during the game? Then simply evolve your 30 HP Tynamo's first. Of course you can Dynamotor any energy you pay for any retreat (and you still have Skyarrow and Switch), but don't underestimate the flexibillity it offers (without being dependant on other cards from your deck).
I also noticed you wanted to include 2 Shaymin UL, but I don't think you'll ever need more than one. In fact, I run one, and I'm considering to drop it if I can adjust to thinking about my Dynamotors even more carefully. I haven't tested it without my Shaymin yet, so I can't tell you a lot about this, but my current list runs fine with 1 Shaymin UL. The trick with Shaymin UL is that you shouldn't ''overuse'' it (or in short, don't grow too dependant on it). See it as the cherry on the pie; it's nice to have, but the pie is fine as it is without it.
I'll explain some suggestions here, not only for the OP, but also for other members who have/had questions about them.
Shaymin EX: A late game finisher (is it even anything else?) with pretty ''fragile'' stats. You don't want to start with it, and it's not that useful at all early to mid game. Also note it requires Grass and/or Prism energy to work, which can hurt your cosistency. However, what it does, it does very well. With damage varying between the 150 to 180 on average uses, Shaymin EX can make short work of nearly anything (beware of Eviolites on EX's though!! Don't forget your Plus Powers can be really helpful here too!) that it has to face late game. When you use it, use it as a ''cleaning mop'' to push through your final one (or two) prizes for the game.
Regigigas EX: Many people are wondering about why Regigigas EX can be useful. It shares the same weakness as your entire deck, has quite ''expensive'' attacks, and is terrible (that is even an understatement) when you want to retreat it. However, with or without Eviolite, Regigigas can sponge a LOT of damage early game. What's more, if you don't fear Terrakion, why not keep plowing with it until your opponent gets it down? By that time you will already have a fully fledged field, ready to smash most thing apart which your Regigigas EX left behind. Even if you fear Terrakion, why not make a lead with it to sponge some damage, but simply don't KO anything? If they are loading a Terrakion manually, simply attach an Eviolite to deny the OHKO, and simply KO it right back. And even when Terrakion is out of the question but your Gigas takes a beating, you can still use it's Giga Power to great effect (especially with Eviolite!) along with Catcher to soften up the harder targets for the rest of your deck. In a Mewtwo War where one of your Mewtwo's is prized, or you simply can't keep up with it, promote Regigigas. If your Gigas is fully loaded, it will take an average of 120 to 160 damage. Enough to revenge KO the Mewtwo back, keeping the prize exchange once again ''even'' in a way. As you can see Regigigas EX has many uses, but it also has many ''problems'' to work with. It is just as easily taken down by Terrakion as your entire deck, and it isn't any more durable than your Zekrom EX. Luckily it works on any energy, and it can even (ab)use DCE. The most scary part of Regigigas EX is that in ZekEels it can come out of nowhere like Zekrom EX (all it needs is 2 Dynamotors + a DCE attach for the turn), ready to take an opponent by surprise an making a huge dent to their field if it's not prepared for such a thing. I think Regigigas actually fits the best of the entire EX-theme; high risk/high reward. Therefore Regigigas isn't for all players, but those who can use it will find great help from it.
Zapdos ND: Boasting an Fighting resistance, Zapdos can be used to snipe an opponent's bench or to ''get lucky'' on some coin flips. Either way, Zapdos is just there as an element of surprise when you start sniping, or threathen their active 130+ HP pokémon with a possible 3 to 4 heads. Just a note from myself, if you play Zapdos, play it for Random Spark. Thundering Hurricane is a nice ''gimmick'' attack, and should really never be used unless you have no better options available. Zapdos is horrible in the mirror match though, as it has an unusual weakness to itself; something I thought was exclusively meant for Psychic and Dragon type pokémon. A well timed Catcher and a lot of Random Sparks can give your opponent a lot of headaces, but a badly timed Zapdos will almost most certainly give you headaces instead.
Stunfisk: Being more and more discussed and considered, Stunfisk can work with the same Electric energy as the rest of your deck, while being a Fighting type instead. Do I really need to explain what benefits being a Fighting type is in this format, as well as the advantage(s) that it runs on the same energy as the rest of your deck? I didn't think so either. It's not as powerful as Terrakion, but at least it's more consistent.
T/S/S
Once again, I don't have too much to point out here, but here are some tweaks I'd suggest:
Supporters:
Your line up looks nice, but I'd still suggest you drop one Collector to up the Junipers to 4. While I know it's crucial to get a T1 Collector, or at least get a few basics to start with, Collector usually becomes a ''dead card'' after the 1st. With all the raw drawpower Juniper and Sage offer you, to me the 4th Collector becomes useless (you'll be discarding it most of the time anyways; your 4th copy). And once again, with the raw drawpower you got, you should be able to draw into your basics.
Another thing I would like to suggest is swap the PONT for N. This is purely player's preference, so it's not really a needed thing, but to me N is an early game PONT, a mid game Judge, and otherwise it's just Junk Arm/Juniper/Sage fodder. But in all of the forementioned cases it offers you disruption. Consider it if you will, or at least try a few games with it the way I suggested it. If you don't like it, just keep the PONT. But at least you can say you know what it's like to play with it like that, no?
As I pointed out before, I would drop the Twins (along with the Thundurus), but if you feel like it's working, you should keep them. Don't let anyone discourage you from trying your own idea's, but don't ignore advice just because you don't like it. Try it at least, and then make your final decision. Either way, play what suits you best...!
Stadiums:
Not much to say here I guess. You run only 1 copy of Skyarrow, and I suppose you (can) use your Twins to fetch it when needed. I'd drop it altogether though, as usually other decks also run Skyarrow, and you should be able to retreat quite easily thanks to your 2 Switch, and possibly the 30 HP Tynamo; all other cases should be managable with the help of manual attachments and Dynamotor. If you want to keep it though, I suggest at least two. And if you keep it, I would also like to point out you can also consider Smeargle UD/CoL as a tech (over Shaymin UL I guess), as Skyarrow makes Smeargle very playable.
Tools:
Even less to say here! You run 2 Eviolite, and so do I. So far I haven't had much trouble with two, and I'm even considering to drop them. However, so far they have proven themselves too helpful to drop them, so I guess I'll keep them myself as well...!
Trainers - Items
I must say, this looks pretty solid. Some players prefer the 4th Catcher, a 3rd Switch, or even Lost Remover and the likes, but this is all tweaking your own list and player's preference. All I really have to add here is that PokéGear 3.0 can be a great help here, especially if you decide to cut the Collector back to 3. My own list runs PokéGear 3.0, and it is yet to disappoint me (the amount you include is of course up to yourself). See what works for you, but I think you have a quite solid base as it is...!
Energy
Well, as promised before, I have something to get back to. I'll start by saying you got the right amount of energy to begin with. There is absolutely nothign wrong with this line up. However, due to the aggressive nature of the deck itself, along with all the ''recycling'' you use, I personally find myself having a ''one energy too much'' problem; I used to run 14 as well, but often I found myself with one energy too much on hand. You might wonder ''How is that even possible? Having an energy too much?'', but it's quite simple really. Often I could only attach one energy from my turn, do the desired amount of Dynamotors, and then I'd have this ''dead'' energy stuck in my hand. I'd often find myself wanting to have something else in my hand in place of that energy. That's why I cut back my energy to 13 instead of 14. This is not for everyone though, and use with caution (I don't advice taking out the 14th energy the evening before a tournament for example).
Otherwise the energy line looks just fine, with the optional exception of Grass/Fighting/Prism energy if you were to include anything that requires different energy.
Well then, I hope I helped you in various ways, and good luck with the deck! My break is actually over as well, so props to me for finishing it in time...! =P For any other advice/questions/etc, feel free to PM me...!
~ James