One reason why I think YGO keeps dipping and spiking is because of it's unlimited format. Because they only ban certain cards instead of rotating out entire sets, there is an enormous amount of replay-ability from past players who want to start playing again. They don't have to worry about all their cards being illegal to use, and can just hop right back in.
With new sets still supporting old deck designs (like zombies, or amazons), these old players are seduced back into the game. So, even when popularity dies down, something small like a new set can suddenly spike the popularity of the game.
That's my theory of course.