The biggest problem I have with GIMP is that it's not intuitive. Every time I open it I have to stop and think how I am supposed to do what I am trying to do, my work never flows.
This has such an impact on my productivity that I'm desperately looking for alternatives that don't involve purchasing Photoshop - now looking at Pixelmator. Other members of the team have switched to Paint.NET or other simple editors, but they are too simple for me.
Another problem that I have is with focus - sometimes the picture window loses input focus to one of the tool windows and then the keyboard shortcuts stop working. I have to click on the window and then use the shortcut, but when clicking the current tool will execute its action (such as paint a black blob in the middle of the layer), so I have to click outside the picture area (might be hard to do) or hunt for the title bar.
Furthermore, when the tool windows have focus they control some of the widgets in the tool window, popping up subwindows or changing settings by accident.
Yet another issue is text editing and selection. GIMP does not allow me to do live text-editing, instead it pops up a dialog box and I have to adjust the actual text rect in the background. Every time I click the text rect to adjust it the tool windows flicker into view for 0.5 seconds, very annoying. Selections are significantly harder to control compared to Photoshop, where you can do pretty much anything to a selection just by using the mouse and one or two keys.
General UI problems:
* dialogs that are too small
* dialogs popping up over other dialogs
* many dialogs that cover the image when shown and I have to move them out of the way
* dialogs that sometimes remember their position, sometimes show up at apparently random locations
* tool windows exiting the screen
* tool fields that just look like they were thrown together without any thought to spacing, grouping and alignment (check out the rectangle select or the almost invisible spinner arrows for the layer transparency)
* the layers tool window is especially difficult to use with a mouse (dragging & dropping, ordering, linking)
* tools that reset their settings (e.g: move tool rests to pick a layer to move instead of move active)
* general disregard for UI design that makes the UI look crowded (e.g layers tab icons)
* the design choice of clipping layers to the visible image area, forcing you to resize the canvas and the layers unnecessarily
I could go on and on and on. I can't remember using GIMP even once without being annoyed by something in the UI that breaks my work flow.
The features I miss the most are adjustments layers, layer grouping (this is so painful when working with a lot of layers).