Part of the reasons for notify-osd is a very elegant and universal notification system. As far as I know, the theme is built into the code and would require a complete rewrite to allow this.
If you want a different theme, you could "apt-get source notify-osd" and change it yourself.
The current notification looks great. Bringing this theme feature should not affect the performance of the app. If it does then I am against it.Just my opinion
Saying that unhappy users should just change it themselves is a cop out.*
If the average user wants to customize the notification system's behavior, are they going to hack the existing system or replace it with an alternative system? I don't think so.
There are legitimate reasons for not letting the user customize the notification system (e.g., feature bloat, option bloat, lack of simplicity/universality). Issues like these are the ones that should be addressed.
*That may be a bit strong, and I don't mean it offensively. But it had to be said.
It's a design decision to specifically not allow the notifications to be themable. I don't know what reason the Canonical devs have for this, but it seems a very weird position to take.
The specifications for Notify OSD state:
"Regardless of type, a bubble should appear as a rectangle of color #131313 (regardless of theme) with opacity 90%, corner roundness 0.375 em, and a drop shadow of #000000 color and 0.5 em spread. The bubble should blur whatever is behind it with a Gaussian blur of 0.125 em."
Despite your wishes, Andrew, gconf-editor isn't used for settings much more advanced than can be configured with existing guis. It's a little hard to learn where things are, but it's really easy to use. You should actually try it before judging it.
This type of feature creep would lead us down a path I don't want to go down. Soon enough Ubuntu would start being as cluttered as KDE.
As for "EVERY" implementation of this allowing theming, "notify-osd theme" is not a very fruitful google search.