I am not an user of gnome 3, so what I am just asking may be obvious to
others.

You say  "Gnome designers decided they didn't want third-party
applications in their panel at all".

Does this mean that apps like skype, wuala, jitsy that require system
tray icons cannot be used at all in gnome 3? I cannot believe this. Does
this mean that gnome 3 whitelists specific applications like ubuntu
does? This also seems strange to me since it means that any app that the
developers forgot to whitelist results broken.

Indeed, it is this the main issue with ubuntu. Breaking all those
applications that are not whitelisted and handling to the user the
responsibility to fix the whitelist by using textual tools that are by
no means friendly to the unexperienced ones.

So in case gnome has a better strategy to the 'blacklisted by default,
explicitly whitelisted', probably ubuntu should consider it.

At least why not using an auto-whitelisting?

For instance. I need to run app XYZ that is not whitelisted by default.
The first time I run it and it tries to set up an icon on the system
tray, I get a notification like "Application XYZ trying to use the
system tray. This is deprecated and the application should be fixed.
Consider filing a bug report about the application. In the meantime
Ubuntu will work around the issue". After this, the application gets
automatically whitelisted (possibly with a timing mechanism... e.g.
whitelisted for 30 days).

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https://bugs.launchpad.net/bugs/773979

Title:
  legacy applications (using system tray) do not work in unity without a
  porting effort

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