As my MTG career is still in limbo at the moment I haven't tried playing a three-colour Tarkir deck, but judging from my general (though modest) knowledge of deck building principles, I can imagine they're a right pain in the behind to balance properly.
From what I've read on the official website this "colour wedge" thing is exclusive to the set Khans of Tarkir and it's going to disappear later down the block. From a story perspective, this is related to the fact that the entire block is going to be a time travel story. The second set will probably involve a journey to a past where dragons had not yet gone extinct. The last set, then, might result in an alternate future, where the clans from Khans of Tarkir were never formed, thus getting rid of the colour wedges that each represent the one aspect of the Dragon around which they were founded.