I can't think of anything that gets cards back into your deck besides Sacred Ash and that Japanese "Energy Returner" promo, so I'll just go with things that can pull things back into your hand.
Off the top of my head, Diggersby XY allows you to pull two item cards into your hand for the price...
Lysandre isn't just for bringing things up from the bench to kill them...It's also very useful to strand things in the active, by forcing your opponent to waste their energy drops retreating the Pokemon you Lysandre'd up.
The reason why this deck works so well against Toad is that it accelerates from the discard. I'm not sure about the whole EX-* era, but I'd guess that Blaziken/Delcatty decks were pretty good against energy denial decks (if they existed) due to most energy denial decks sending energy into the...
It seems that everyone is understating the importance of Hoopa-EX, in terms of EX based decks. The ability to search out 3 EX cards is incredible, as it's a free Pokemon Collector (not even Fan Club) for the majority of your deck, including the ability to search out draw support (Shaymin-EX)...
Eh, there are plenty of times that I've said, "Oh, I would really like to remove THIS card to substitute this in for THIS card, but the second card only works well in some matchups, while the first card works better in more matchups."
This is something I'm incredibly interested in, and I'd love to hear about more decks. I looked on Bulbapedia, and they have a list, although I don't know how accurate it is, and most of the decks don't have descriptions.
There have already been cards w/ 2 weaknesses and resistances (not sure about three). Although almost all steels would be very hard to include their resistance.
I just don't want KSS to be in rotation. Toad Decks are fine w/o energy denial, as you can at least somewhat play the game and have a chance to come back from Item Lock, but with Crushing Hammer in the format, that will be difficult to do.
The only hope Vir/Gen has against Toad/Puff is getting the req'd energy cost to Emerald Slash. If the ToadPuff can manage to Head Ringer the Virizions and the Genesects, and can manage to prevent 3 Energy from going down on a Pokemon, the ToadPuff player should be good.
Also remember you're playing a Metal deck, even if you only have a few attackers, a few can go a long way, especially if you've got Heatran swinging for 200, Dialga going for 240, or Aegislash for 240 (MB).
I already reported this as a bug during the battle, but a Hawlucha with a Strong Energy attached used Flying Press for 80 damage against my Aegislash-EX without there being a Silent Lab or Garbodor in play.