DathPika is right-- I honestly can't even remember the last time I or an opponent lost by decking out, and I also can't remember reading/hearing about it happening elsewhere in forever either. Winning via stall is almost a lost art, especially in timed tournaments. It is too easy for your opponent to get a few prizes (or even just one if you're completely playing defense the whole game) and then win on time long before they ever deck. Claydol and Kingdra have both already been mentioned as anti-deck cards and it is true that they excel at decking prevention, especially Claydol (which you'll see in virtually every deck). There is also Night Maintenance, Uxie, Team Galactic's Wager, etc..
I used to play back during those days when Chansey/Alakazam/Pokemon Center/Scoop Up/Mr. Fuji/Mr. Mime etc. were legal. However, even then it was not common to deck your opponent out, unless you included Moltres in the mix. The best stall decks also had an offensive component that they could apply, ie. Alakazam decks would attack with Mr. Mime and slowly but surely build up to big Meditates while keeping it alive via its Power and Damage Swap with a Chansey-filled bench. The reason that kind of deck never really could compete in serious play was that it was too easy to Gust of Wind in the Alakazam and take it out, or simply bring in something that had been heavily Swapped to and get a KO on it, only to be repeated via Item Finder/other Gusts enough times to either win on time or simply take 6 prizes. In this format, you don't have any damage swappers anyway (Cresselia lv. X does not count) and even if you did, there are plenty of Pokemon capable of getting OHKOs (Mesprit lv. X, Infernape MD, Rayquaza, Kingdra, etc.), so you need some way to do damage and take prizes while you stall, if you're going to go that route.
All that being said, Rhyperior is intriguing in the same way Moltres used to be if you devote your deck over to it. It is about the only way you are going to even have a chance of decking your opponent. Flygon lv. X from the next set after the one we'll be getting early next year may also interest you.
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Oh I forgot about Gyarados SF. That is another way to discard cards from your opponent's deck while also dealing damage. It's flippy, but there may be turns when you get 2+ heads and that combined possibly with Rhyperior and Super Scoop Up could be a fun deck if not a super competitive one.