The # of in-game boxes will probably be at least the same, if not more, than B/W.
Gen 3 = 386 Pokemon species = 14 boxes @ 30 apiece = 420 slots
Gen 4 = 493 Pokemon species = 18 boxes @ 30 apiece = 540 slots
Gen 5 = 649 Pokemon species = 24 boxes @ 30 apiece = 720 slots
Gen 6 = 750+? Pokemon species = ?? boxes @ 30 apiece = ??? slots
Excluding that Gen 4 anomaly (I stand corrected), the box slots have always had more slots than the available species. Gen 6 will, I'm predicting, have 30 in-game boxes, resulting in 900 slots in-game. That should be plenty. They could get away with 24, but they have enough to bump it up to 30. 30 is also a nice round number, so it can work out. They could do 27 or 28 boxes, but 30 seems the most likely.
(Do not take any of this as fact. This is merely speculation.)
Though I will admit I am one of those people who had to continually clean out his boxes in Black 1 because of overcrowding.