I'm fairly sure that 'Open as Layers" allows you to open multiple files at the same time as layers in a single images, instead of opening and adding each individually. Open will open an image with all its layers as you would expect, it won't flatten it. Feather and Distort operate on the selection, so being under Select makes sense.

I'm probably out of date. Used to be, you had to have plugins to open exotic formatted files like "pdf"; initially the plugin for that just imported the flat bitmap. But that was long ago.

> Running a script is under 'Filters' for some reason.

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?

I can answer these. But consider: the fact that it seems confusing it the whole issue here. Not that it makes sense to you.

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.

Please don't blame Blender for that! ;)