And note I am using Gimp 2. So these things may have changed.
Scripts: I would imagine these would be under Tools.
A quick survey of apps show that options and settings are usually under Tools. Or Files.
And the Plugin Browser is an odd bird. Its details I struggle with when writing scripts. Its reasonable that a database could be under Help. I need it when I'm writing scripts, and no other time. And there's nowhere to go from there - no 'copy example to cut buffer' etc. I'm accustomed to viewing it from a Script console, so I can construct each argument. But not a thing I'm ever going to browse like other Help items.
Admittedly, nested menus is a fairly opaque way to categorize features. Everything is hidden unless you 'open the little door' like an Advent calendar. You can't search for anything without just doing a click-fest down the row. Its a shortcoming of the paradigm. Why others turned to the hated 'ribbon' etc - to make feature-hunting more transparent.
You mean the script console? Where would you rather see it?
> To undo a brush, that's under 'Windows' inexplicably.
Er... I'm not sure what you mean here. Could you elaborate please?
> Filters like Feather and Distort are under 'Select'.
Well, they are not exactly filters, and they affect the selection rather than actual pixel data.
> Keyboard shortcuts are under 'Edit'.
We don't have a Settings menu :)
> The Plugin Browser tool is under 'Help'
Where would you place it?
> My favorite: 'File' has 'Open' above 'Open as Layers', as if you'd more commonly want to destroy all your image layer info when opening an image file.
I'm not sure I understand your reasoning.
> In fact, with 'flatten' there's no need for 'Open' at all?
Why?