First off, this is a cool deck. I love a good Toolbox deck, but even for a toolbox this seems quite spread out.
Next a couple of questions:
How do you deal with Parallel City?
How often do you use some of these 1-of's like Fisherman, Energy Retrieval, VS Seeker?
Next a brief analysis:
Your main attacker is Xerneas you say, but you only have 2. I would recommend upping that to 3 or 4 to have for when they fall. Relying on the one Super Rod to get them back may trip you up.
Xerneas - 120HP
(Y)(C)(C) Rainbow Force: 10+ 30 for every different type on your bench.
So this attack has various levels depending on your own bench. It is a decent attack with a few drawbacks.
Lets start at 3 different Poke's on your bench: 100 damage is
+good for most basics pre-evolution (if you can get them), or a 2HKO on most EX's
-takes 3 shots to KO a Mega and it you're facing one, you won't get 3 turns to kill it
+can be upped to 120 with a Muscle Band or Giovanni's Scheme, taking out most Megas in 2 hits, and killing some support basics and stage 1's (like Trevenant, Bronzong, and Aromatisse)
-Just short of taking out major threats at 130HP (like Shaymin EX)
+easy to get this high, if you went first this is an easy turn 2 hit
With 4 different on your bench: 130 damage:
++ this is a great damage level, taking out huge support like Shaymin EX, Garchomp (BREAKthrough), and Yveltal (XY)
+2HKO on most EX's and Megas
With 5 different on your bench: 160 damage:
-maxed out a normal bench, difficult to maintain, and just short of OHKO on most EX's
+muscle band brings this into OHKO on most EX's
With 8 different: 250 damage:
+huge hit, and there is plenty of pokes in this deck if you can get them out
-no room for multiple of the same type, aka Jynx and Mr. Mime and Golurk, Gallade and Golurk
Lets also talk about that second attack, because it is worth mentioning:
(Y)(Y)(C)(C) - Power Creation: 80+ 80 more if this Pokemon was healed this turn
This is an expensive attack, but with Jynx on your bench, it might be worth it
+you have the healing support you need to get the +80
-you need to be damaged first, and with 120HP that is possible but dangerous, as there are many threats out there that would eat you right up
+with Muscle Band/Giovanni's Scheme you get into OHKO range for most EX's
Recommendations:
- Gollet/Golurk: unless the multitype counts as a unique typing and distinguishes it from the other psychic and fighting types, this poke is redundant
+ Raltz (of another type) /Gardevoir AOR/ rare candy: this brings in another type potential (although it's another fairy) and extra heal support for when you'd rather have Mr Mime
-Fisherman, Energy Retrieval: you don't need this much discarded basic energy recycling, you might be happier with Energy Recycler AOR if you find you really have all your energy tied up in your discard pile
-Switch: you have retreat support with Dodrio
+Level Balls!! More level balls to get all the bench support you need when you need it
-2 Rainbow Energy: you should rely more on your main attackers and secondaries that require DCE, losing all of them might mean many of your benched pokes are not attacking, but their attacks are useless anyways
+2 Double Colorless Energy: to support your main attacker, as well as most of your secondary attackers
-Illumise: she is far too situational, requiring you to have a rainbow energy to use and it terribly frail
+Combee/Vespiqueen: a late game hard-hitter if you were forced to discard a lot
-Pokemon Center Lady/Healing Scarf: you have enough healing support to use it when you need it
+Unknown AOR: acts as psychic on your bench when you need it, then a free draw. Also helps boost Vespiqueen
-Super Rod: also about the energy, but replacing it with Sacred Ash FLF might make your day easier
-Hard Charm: see below
+ Fighting Fury Belt: attaching this to your Xerneas will give it the extra HP it needs to be more viable, and +10 attack bumps up many of the levels to key points. This card is situational compared to Muscle Band, so you'll have to see what your opponent is running to optimize it.
*Strategy: get that Octillery out ASAP, that's key for drawing the cards you need to fill up your bench and all those situational cards.
Overall, this is a cool deck, looks like fun, but you may want to narrow your focus a bit on what hits hardest and provides the support you need. What you use every game is more important than what you might need in certain situations.
