I would emphatically disagree with the idea of banning a card or combo. From what I can see, all the "I win" combos that are essentially undefendable (e.g., emptying the supply on Turn 4 without any cards that would let your opponent mess it up) have almost negligible chance of occurring. I would guess that a player that went for a turn like that would likely lose most games, since they aren't making their deck towards a high-win-percentage strategy. And if both players went for it, you'd probably just see a sub-par game.
More common strategies and combos (e.g., Masquerade pin) are neat, but I don't think they're the dominant strategy almost ever. I thin most experienced players that play in tournaments would be able to defend against it, or play it themselves if it's a good idea. And if not, well, make tournaments match format (which, I think, most are). The chance of a crazy combo existing in two random boards is pretty small.
And if you're still concerned about it, well, there's Veto Mode. I would imagine it would be pretty rare for there to exist a game-breaking combo that requires only two out of three particular cards. (Say you want to ban it and your opponent doesn't).