As powerful at it may be "Set Matte" has some limitations and it is not very easy to use. More often than not you still need one layer as mask for another layer. Even simple setups become layer-salads.

My ideas to upgrade this effect:

• timepoint of layer matte should be accessable via Expressions/Keyframes. This way we can use one single precpomped Animation to mask as many layers as we want
• also 3D layers should be able to be masked by a 2D animation using "Stretch Matte to Fit"
• To use this effect I always have to precomp my footage and then "collapse transformations". There could be more intuitive ways, more resolution-independent -> like it already works with Shape Layers.