Even if most Ubuntu users aren't at all tech savvy, you can't annoy the small minority which are power users. Those are the people who may decide to get involved in development and submit patches, so their opinion is critical to your success.
How about, for starters, adding a gconf option to show an X icon on notifications. I personally think it makes sense not to have one, but if people want one then you should let them have it. (And normal users, who you're trying to train to use notifications in a specific way, will never turn on the X because they don't even know what gconf is.)
Either way, thanks a lot for all of the work that you guys have done so far! It's great to see Canonical getting involved and trying to improve the user interface.
Natan