1. Several countercards exist to Emrakul being cheated into play. Obviously Emrakul is at her scariest early in the game where she can threaten to quickly annihilate most of a players board, this is basically the way she is played in the 60 card, 4 copy formats modern and legacy. Hoever, there have been several cards printed that strait up hose trying to cheat a creature into play. Most notably Containment Priest.
2. Protection from colored spells isn't actually that good anymore. Sure, you can't just Swords to Plowshares Emrakul, but there are plenty of good removal spells that can deal with her. WE've had several printings of better style Oblivion Rings, lots of planeswalkers can kill creatures, way more wrath effcts now then there used to be, we have colorless removal spells, Cyclonic Rift is the #2 EDH card behind Sol Ring, and there are fantastic EDH cards like Crackling Doom and Profane Procession that somebody will often be back packing in their decks.
3. Annihilator 6 isn't that good anymore either. It seems like MTG has been really gungho on the tokens as of late. It seems like every set we get some new type of token, be it treasure, clues, gold, or just creature tokens that decks are so capable of flooding a board with so many paper tokens that we politely ask them to just use a dice. I've been playing with and against the other OG titans Ulamog and Kozilek and I've had cards like Smothering Tithe, Curse of Opulence, Spell Swindle, and Nesting Dragon just completly absord annihilator triggers through multiple rounds of combat. Let's not forget about Teferi's Protection either.
Quote from Sheldon »You're the reason we can't have nice things.