I've noticed that Pd has some very basic user interface flaws, both on Mac and Linux.
Mac: There is no way to quickly cycle through open windows. Command-~ is the standard way to do that on a Mac. Instead, you have to go to the "Window" menu and select which window you want. Very cumbersome. Also, if a patch was built on a computer with a screen larger than yours, the patch opens up with no way to find the lower right hand corner resize handle because it's off the screen somewhere, and you're kind of stuck not being able to really use the patch. The full screen/zoom button in the title bar has no effect, when it should really collapse the window size down so it fits on your screen. Also, the color picking boxes do not show their colors on Mac - they just appear as a grid of generic gray buttons and you have to guess.
Linux: When you close a patch, a box pops up and asks you if you're sure, but it seems to be attached to the main Pd window and usually gets hidden under a bunch of other windows, and you have to do a bunch of extra clicking around just to close the window you wanted to close.
Both (I think): Pressing tab in a dialog box, like the properties for an element, does not move you to the next field. It is a real pain to have to select each new box with the mouse instead of just pushing tab.
Any others?