Show tray apps in overview.
Gnome's removal of the "legacy" system tray doesn't solve the problem of daemon-like applications. There is an inherent need for such applications and this means there is a need for something like the system tray. Android has one, windows has one, OSX has one. These daemon-like apps are different from normal ones: they don't need to have a window open and they cannot in principle be associated with any workspace. At the same time, these apps are no background services, which run without any user interaction whatsoever.
The user needs some way to tell that these "Special" apps are running. I don't want to dig through the system manager to see that Skype is open (or "offline"), or that that a downloader is hogging bandwidth. But I also don't want them open and cluttering up the overview and dock. That's what a system tray was for.
Gnome axed the system tray a year ago and not a single app - to my knowledge - has found an alternative way of telling the user that it's running without a window, never mind communicating state and providing the options that are traditionally exposed via right-click on the system tray. People have taken to writing extensions just to reproduce the functionality of particular tray icons, which is absolutely ridiculous. Meanwhile, users are installing the appindicator extension to restore the missing functionality and Ubuntu is shipping it by default. Appindicator is just like a normal tray only worse: it lacks the ability to hide icons.
Something is clearly not working.
TL;DR. I understand not wanting tray icons to pollute the panel. This means their function has to be transferred to some other place. Currently, the "solution" is to just to break Gnome's design 100% and install appindindicator, which irrevocably pollutes the panel.
There is plenty of room in the overview. Why not just put the tray icons on the bottom in the overview? Isn't the function of the overview to show running GUI applications? If so, it must show these daemon-like applications, otherwise it's not doing its job. It's not like there is no space for them there.