Real shortly then: broken but not-yet-replaceable applications needs two things from their indicators:
1. to be able to interact left/right click etc
2. to be able to be seen at all times
That's it. Otherwise they break the *experience*. As described, above. Not unusable, but it's a definite regression, and as I see so far it seems mostly just "because", and I think it's a bit strange when it doesn't make it fit more into the whole anyway.
that's your POV, not necessarily fact.
Fact is, we are bringing consistency and design to the panel.
I see nothing wrong with keeping notification area as a panel applet you can install manuall, e.g. when installing Wine.
Things change all the time, and apps have to adapt to that all the time, regression is perhaps the correct term for this, but this is not an error, since we are well aware of it.
I never said there couldn't be a new way of doing it, only that those suggested does not fulfill the need. Keep on keeping on.