Mega Sceptile's Theta Stop ability only negates abilities that directly affect it. Cards like Giratina EX and Carbink do not do anything directly to M Sceptile, instead their abilities place effects upon themselves to negate incoming damage. So no, you won't be able to attack Giratina EX with Mega Sceptile unless you shut off it's ability. Although that shouldn't be much of a concern for you since Ariados + Sceptile EX takes care of Giratina EX easily. And according to your list Carbink can also be dealt with by using Mew to copy Sceptile EX's attack with Ariados in play.
Here are some suggestions for the list you posted...
-1 Lysandre: 2 should be enough and playing 3 risks clogging up your hand with too many non draw supporters
-1 Pokemon Ranger: Once again I think playing just one copy should be enough, its a dead card in most match ups
-2 Super Rod: Don't really see the need to play any Super Rod in this deck. You already have solid energy recovery and the only benefit would be to help recover after attacking with and losing a Mew. But your priority should always be your Mega Sceptiles anyways.
-1 Energy Retrieval: I'm personally not a fan of Energy Retrieval. I don't play any in M Sceptile variants and I have never wished that I included it. I realize that it has its uses and can be more than just a dead card, but Mega Turbos and Fisherman have provided me with all of the discard retrieval I've ever needed. I left one in the list because its still a decent card that can be useful but feel free to remove the second one for either another Mega Turbo, Trainers' Mail, 2nd Mew, or 3rd N.
+1 Fisherman: Just knowing that you can play this card in the mid to late game can allow you to be a bit more aggressive with your energies. Especially in the later stages of the game when all you need are energies to keep the loop going for a few more turns. Energy Retrievals are nice but with Fisherman you actually don't mind seeing him early since you can just discard him and remind yourself to save a VS Seeker for him whenever you need energy. Energy Retrievals can be dead cards early on or only be able to get back 1 energy at a time.
+1 Mega Turbo: Together with Fisherman these cards can really open up your deck. You won't need to be cautious about discarding energies and the Mega Turbo can actually accelerate your Mega Sceptiles, possibly allowing them to attack the first turn possible or to keep them going if you could only attach one energy with Jagged Saber the previous turn.
+3 Trainers' Mail: These should absolutely go in. Speed. Speed. Speed. They can let you reach for Forests, Spirit Links, or Ultra Balls all cards that are vital to playing with good pace within the meta game.
Overall, I like the list. It's a bit different that what I've been playing lately but it should still perform well against anything not named Volcanion. The 1 level ball seems like an efficient way to get your Ariados line/Mew into play which is nice, not sure if its worth playing over other cards but its still a solid pick. Shrine of Memories is nice, I like that one as a one of, just have to be mindful that it can be a double edged sword if you're playing a deck with evolutions in it. Oh and I would also consider playing a single Assault Vest. There is a lot of Special Energy going around right now and since you can evolve on your first turn with a Forest of Giant Plants without a spirit link it can save your M Sceptiles life against stuff like M Ray, Rainbow Road, and even M Mewtwo. I'm also assuming you have no way to get a 2nd Shaymin EX, right? Because if you can, you should absolutely get a 2nd Shaymin. One can work though, just gotta believe in the heart of the cards haha.
Anyways, sorry about writing so much. I get carried away sometimes when giving advice to people since I really try to help them see how I perceive certain cards and my logic behind it. I'm by no means a Pokemon Master or anything but I feel as if I have a solid grasp on the nuances of the card game and the thought process behind creating a deck list. That being said, I hope you found all of this useful. Feel free to let me know if you incorporate any of these changes and whether or not they're working for you.
Good luck!