Here's an idea: Just leave the notification icons in the panel. They
should show up right next to the existing indicator icons. This could
be done in the same indicator-applet or in a seperate
notification-area applet, it doesn't really matter. What's important
is that they should have the full, normal, legacy behavior of
notification icons, right down to tooltips and
left/middle/right-clicks. Everything works just the way people would
have expected 2-8 years ago.
For ubuntu's purposes, you just make sure none of the major
ubuntu-supported applications use the notification area API. If the
user doesn't run anything with the notification area API, they'll
never see an icon there, and it'll never take up any space, and it'll
never feel inconsistent. If they do use applications that aren't
ubuntu-supported, they'll work, just with a little less consistency.
This seems like the best idea. When using Wine to get non-standard applications to work, you are consciously stepping outside the regular experience and some inconsistency is expected.
I'm all for deprecating and forcing applications to modernize and fit in, but only when there is an actual chance it may happen. Breaking the now working experience of non-controllable but common use cases seems too much like punishing the user because there is no substitute application in Ubuntu and can only lead to a bad experience.
/ K