Comment 1 for bug 1389895

> "Every" other application (on Windows, at least) prefers the order Ctrl, then Alt, then Shift.

GTK based applications -such as Inkscape, Gimp, Geany and probably others- conform to the Gnome Human Interface Guidelines (https://developer.gnome.org/hig/stable/keyboard-input.html.en#access-keys), even on Windows.
Changing the order would generate inconsistencies on GNU/Linux systems (I don't know what's the preferred order on OS-X).
We could also detect the operating system and change the order for Windows only, but it wouldn't be nice for people working on documentation...