It's not a matter of revision.
It is a matter of tier.
The asus X99 Deluxe is the top tier X99 (non gaming) Asus Mainboard.
As such, it offers the biggest amount of extras and the highest quality components.
The X99-Pro is the Middle tier. It has a bit lower quality VRM components.
The X99-A is the bottom tier board. As such it offers the least extras.
For reference, the X99 Deluxe is top.
X99-S is the deluxe in board design and components but missing extra features (Wi-fi, Ethernet)
X99-A is X99-Pro in board design and components but missing extra features (Wi-fi, Ethernet).
The cooling solution on the X99-Pro is the same as the Deluxe, but the circuirtry is the same as the X99-A.
in regard to VRM:
X99 deluxe = X99-S > X99-Pro = X99-A.
Hope this helps clear the differences.