Now that decision is to not have a Edit | Preferences window https://bugs.launchpad.net/pinta/+bug/671874
I am asking myself if there is really need for Layers | Layer Properties window. It looks to me the same way as Edit | Preferences.

I think there is no need for Layer Properties window why, because there are only three settings in Layer window that could be simplified:
1. Visible checkbox is duplicated, because there is already a checkbox in Layers panel (tool window).
2. It would be nice if renaming the layer will happen just like Gimp has, double click on layer name in Layer panel and edit box is embed (appears on the right same position) into text box itself. So renaming layer and pressing and Enter key.
3. Opacity could be solved just like a zoom window is in toolbar. So having drop-down box with some of the most important values like 0, 10, 20, 30, ..., 100. And make it possible to manually enter text into field and manually change opacity to desired value. So the same behaviour like zoom drop-down box.