Disc brakes are:
-Heaver
-More expensive.
-Complicate wheel removal/installation particularly if you have to change a road-side flat tire.
-Require a stronger (read heavier) fork and reenforced rear stays.
-Hydraulic versions are prone to fade from excess heat on long downhills. (more of a problem for road bikes than MTB use).
-Require proprietary pads that are more expensive and more difficult to find.
-More sensitive to minor mis-alignment
They do have improved wet braking although good double pivot rim brakes with good pads aren't far behind. Your point about lack of rim damage is valid but only on bikes used routinely in bad weather or in harsh off-road conditions. On road bikes used in mostly fair weather I have rims with well over 25,000 miles still in good condition. The argument that disc-only rims could be significantly lighter isn't valid. Rims are designed for adequate strength and rigidity and the additional material added for brake track wear is minor.
So, for MTB, Cyclocross and all-weather commuter bikes, perhaps disc's advantages do out weight their several disadvantages. But the desirability of their universal application is far from obvious.