Matthew Paul Thomas, a Canonical employeee working on Ubuntu's design team, had just sent the following message to the ubuntu-devel list:
It's not all or nothing -- it's been a very gradual change.
In April 2010, we announced that we would be retiring the notification area in Ubuntu 11.04.
In 10.04 and 10.10, Ubuntu allowed both notification area items and application indicator items.
In 11.04, Unity reimplemented the notification area with a whitelist, a whitelist that is longer than we originally intended.
In 11.10, if people have time to work on fixes for HPLIP and Mumble, we'll be able to shrink the whitelist. (And by then we'll have a real developer site, where ISVs can more easily find information about application indicators and other Ubuntu APIs.)
The comments regarding the Ubuntu 11.10 are what's interesting. Evidently by Ubuntu 11.10, there will be a "real developer site" for "Ubuntu APIs."
One of the gripes among mainstream ISVs with regard to Linux is the lack of -- proper -- documentation and stable APIs. Canonical may now be attempting to correct this, but for some it may be a concern that this site is for "Ubuntu APIs" if Canonical continues pushing out their own APIs (such as for the application indicators) that may not be fully supported upstream by other Linux projects and distributions, still leading to a fragmented mess.
Ubuntu 11.10 is codenamed Oneiric Ocelot and will be released this October. When we have more information on this expected Ubuntu developer web-site, we'll pass it along.