On the one hand I'm thinking you might be misinterpreting some things, but on the other hand, if you are misinterpreting them, so will others. So something should be done to clarify the UI. But perhaps I should resort to a usability expert (hey, I know one of those!

I wonder if improvements can be made without rethinking the whole interface. Anyway, here are my comments on your comments:
The inconsistencies I find most are when I double-click on some things, it opens the properties, but when I double-click on other things, it opens the editor window. Rather than having a sub-item in the tree to edit those objects, I'd think just have a Properties item in the right-click menu to access the properties, and double-clicking always edits.
Would you eliminate levels from the tree as you do that, then? I thought the node's name/location in the tree made it clear that some were opening editors. But if it's possible to edit a graphic sheet from the same node where you define its parameters, there wouldn't need to be an extra level, right? The thing that makes me nervous about collapsing that is that people may then find it more difficult to figure out how to edit properties of an object. They might think that once it's added, you can't change the properties you saw when adding it.
For the Frameset editor specifically, the text arrows via ^, <<, and >> are kind of kludgy. I'd either put graphics on them, or, more preferably, an overhaul of how it works.
Yes, every time I see the frameset editor I wonder "what I was on" when I designed it

. I must have intended to go back and improve it at one point -- perhaps expecting some better button graphics from OrionPax. But I'm not sure what to do about it.
First, get rid of the ^Load^ and ^Add^ buttons. The drag-and-drop operation is sufficient, I think, and the buttons make it more confusing.
I make it a rule to never rely on drag and drop as the only way to accomplish something. I do think the buttons should be removed, but there should still be a way that doesn't require manual dexterity or even a mouse to accomplish the task. So maybe I should remove the buttons, but then add the commands to a menu, and have keyboard shortcuts on the menus maybe.
Many of your other suggestions for the frameset editor I agree with.
Dragging from the frame editor to the frameset view to save a frame should allow the user to overwrite the frame they dragged it onto, or insert it in between if they drag it between frames.
If I do that I'll have to make the spaces between the frames significantly larger to limit the risk that someone accidentally overwrites a frame instead of inserting it. And if I make it behave that way there, it would/should behave that way everywhere, and I'd have to increase the spacing everywhere, reducing the amount of information that you can fit on the screen. But maybe I can use drag modifier keys (Ctrl/Alt/Shift) to determine whether an insert or an overwrite should be performed. Would overwrite be a better default than insert, and then hold Ctrl to perform an insert (with the common "+" indicator on the mouse when inserting)?
I think the Apply button is unnecessary.
The apply button delimits transformations. For example, notice the difference between scaling and rotating a frame as part of the same transformation versus scaling the frame, applying that, then rotating it. If you don't apply the scaling first, you're effectively rotating the image before the scaling (which, I guess, is consistently the apparent sequence/behavior of a matrix transformation), whereas you might want to rotate the scaled image. In making SGDK2 easy to understand for beginners, I don't want to take features/power/flexibility away from the experts unnecessarily, because I fear it will end up still being too complicated for beginners anyway.
The intention was to represent the controls above the buttons as intended modifications to the matrix, and treat the controls below the buttons as the persisted transformation/information. So once you apply the current changes, they are "persisted" to the matrix and then you are once again treating it as an untransformed frame which you can manipulate as you would the original graphic. Is there any way to make this clearer; I think it's an important feature, isn't it?
The slider for rotation almost disappears where it is. Having the textbox below it makes it look like they are unrelated, and having the slider right below the editor area, I often forget it's there.
What would be better? I worry that making the slider any shorter will reduce the resolution of the slider. I myself don't usually use the slider just because I want to rotate frames to specific numeric increments anyway. Do you think the slider is important enough that it needs to be more visible?