Puppet Tool needs a feature that gives you the option to create a custom mesh.
For example, I'm currently animating a image where the eye is blinking. The deform feature for the Puppet tool is perfect for this, but I find that the auto mesh that it creates generates triangles that result in artifacts and are not ideal; the fix for this is just add more points. However I think it would be great to have a feature to draw your own edge loops. Say you can draw a few masks on the image for the the grid/loops, then have the tool generate a mesh based on those guides. Or say just draw one loop then let the tool fill in the gap.
Christopher Unger commented
Here is an example of what I'm talking about, if i missed it let me know if this feature exist ;)