It seems part of the design of the program, that all windows except for
the icon disappear  when the focus is on a window that does not belong
to the program. This makes it pretty hard to use the program, when focus
follows the mouse pointer automatically instead of changing only when
another window is selected by a click.

There should be an obvious option to change this behavior - default
for linux systems should be persistant windows, that do not vanish when
focus is lost.

Additionally, a "right-click" on the icon opens up a menu *behind* the
icon and without honouring the borders of the desktop (most of the menu
is outside the viewable area, most of the viewable part is behind the
icon)

 > It seems part of the design of the program, that all windows except
 > for the icon disappear  when the focus is on a window that does not
 > belong to the program.

No this is part of ApplicationKit (gnustep-gui), not of the program.

 > This makes it pretty hard to use the program, when focus follows the
 > mouse pointer automatically instead of changing only when another
 > window is selected by a click.

Neither focus follows mouse nor autoraise window should be active
when using applications that are built on GNUstep. This is part
of the design.

You definitely want to read:
http://www120.pair.com/mccarthy/nextstep/intro.htmld/

 > There should be an obvious option to change this behavior - default
 > for linux systems should be persistant windows

I disagree, hat has nothing to do with linux systems. Besides Debian
is on the way supporting also non-linux systems (GNU (Hurd) at least,
some are working on GNU/kFreeBSD).

Can you give any reason why this should be an default for graphical
systems?

 > that do not vanish
 > when focus is lost.

You have the sources for gnustep, feel free to write a patch. Good luck.
If you have a working one, I am willing to test it.

 > Additionally, a "right-click" on the icon opens
 > up a menu *behind* the icon and without honouring the borders of the
 > desktop (most of the menu is outside the viewable area, most of the
 > viewable part is behind the icon)

Well there are window managers and there are graphical applications.
What window manager are you using? It's behaving like its original
(mostly). On my Window Maker, the menu doesn't open behind the icon
(which is called application icon). about the menu placement on
right-click, that depends where you place the application icon, and
then whether your window manager handles scrolling of these windows
(this menu) into the viewable area (Window Maker can do that, and
I think the option is on by default).

I hope you can enjoy the software anyways. There is no simple way (known
to me) to get that working like you want it.

Regards,