1-The Merge button at the bottom of layer panel , I really think this should be only one function: "Merge down", so when you click it, it directly merges the layer(s) without a dialog. this will make the workflow faster merging multiple layers etc. I think users will not need "merge visible " so often, and it can be available from the Layer menu on top. would you consider that?
2-A simple floating color wheel panel similar to that would be great.

3-Have extra buttons at the bottom tool bar while in Painting tool, like "Hide selection", "clear selection", "Transform".. it would be nice to have some functionality
while you're in the brush tool, as simple buttons on the bottom tool bar.
4-Add 'invert' to the Mask settings? and remove "reveal all'' and ''hide all'' dialog , assume it's always "reveal all" by default. then the user can invert if he wants the opposite.
5-Please add 'lock transparency' button on the layer panel itself without going into the additional menu. it's a common functionality and needs a faster workflow with one click.