Cause of Wallace line
So all this leading to my question: What could have been the cause of
  the this deep divide?


Think about what animals need to travel between Islands.  It's very difficult unless the water between the islands either drops or freezes over (Deer, for example, have crossed from New Jersey to Staten Island when the Hudson River freezes over), but the ocean doesn't freeze near the Wallace line.

Or, during ice ages when sea level falls as much as 410 feet, Islands can be joined as sea level drops.   Japan, for example, a land-bridge formed through Hokaido to mainland Asia.  Likewise, the UK connects to France and the Bering Straight becomes land as well.

There's nothing particularly remarkable about the water over the Wallace line other than it being too deep for any land bridges to form during ice ages.  The relevant geological feature for land bridges is shallow oceans/seas/bays/straights/channels, etc.   The Java sea is sufficiently shallow that all the islands Northwest of the Wallace line are joined when sea level falls.    

It was pointed out that it's rough water too, but that's not the primary reason.   The primary reason is simply the ocean's depth and width.  Animals have little incentive to try to cross any fairly large body of ocean.  Animals sometimes migrate across raging rivers, but in that situation the other side is clearly visible.  The islands on each side of the Wallace line, even with the sea level drop, would (I assume), appear very far away to the eye, if they could be seen at all.