The list looks more correct but I still find some issues with it. I really think you should use a .5 tier systems just to break the decks apart that don't belong to either, like Smogon's BL tiers that exist for things not exactly OU or UU.
Tier 1:
M Mewtwo EX
Turbo Darkrai
M Rayquaza EX
Darkrai Dragons
Yveltal EX (Should move down a half tier)
Decidueye Plume
Tier 2:
Vespiquen (should move up a half tier, though the placement is fine)
M Gardevoir Despair Ray
Waterbox/ Lapras GX (Should move up a half tier)
Rainbow Road
Volcanion EX (should move up a half tier)
M Scizor EX / M Scizor EX (Should move down a half tier)
Vileplume Varients / Lurantis (I think all Vileplume decks should be at least tier 1.5)
Tauros Giratina
Tier 3:
Umbreon GX
Greninja Break (Not sure how I feel about this. It's still very strong)
Gyarados
Passimian (Seems about right)
Solgaleo/Lurantis (Should move up a tier)
Tier ?:
Pidgeot EX (can't say I like the list. Has an identity crisis. I believe its tier 2 at best)
Espeon GX (Not sure what this deck aims to do)
Houndoom Mill (Should be tier 2. Disuption and mill is strong.)
Let me answer some questions with the deck first.
Pidgeot: The I couldn't find a proper deck list so I decided to make one up on the spot to give people a general idea, I am going to remove that one and replace it with a better one after I finish practicing 5 other decks on my queue. ( I practice every deck I post and for ones I can't find I try to make a deck list and play it vs the other meta decks.)
Greninja Break: This deck indeed is very strong and I believe it will move up spots after leaf blower is released as it will be able to deal with garbodor which is the biggest problem atm.
Vileplume Varients: The problem with some Vileplume varients is consistency the problem with Lurantis is theres not much too it Do 120 Damage heal 30 Hope you don't get 2 hit.
M Scizor EX: This deck has great potential but the increase of volcanion and the consistency is the only problem with this deck, I just believe nobody has found the correct way to build this yet and that's why we don't see it at all. This deck can very easily beat the Tier 1 decks but as stated above Consistency is an issue therefore I think Tier 2 is a solid place for Scizor.
Espeon GX: It's hard to say where this deck belongs It's in a rough position where it has the potential to be good but the cards we have in the format are better.
Houndoom Mill: Mill and Denial Decks are my favorite I wasn't sure if there was a place for them in this format since I have not played any Mill since Sableye Trickshovel.
Waterbox/Lapras GX: I'm sure this is a tier 1 deck but there hasn't been any placements for it other than Anaheim. Hopefully when aqua patch comes out we will see some of the top spots have Waterbox.
Yveltal EX: This deck is still very strong as it can 2 Hit anything in the current format and most of the time Yveltal will have the lead if the game turns into a 2 Hit Match-up.
Now regarding the .5 System I started this with just a Tier 1 2 3 because we had little decks to cover. If the community wants to see a .5 System then I will do so but I believe it will cause more confusion to the newer players than help them understand a Tier list and what are the best decks in the current format.