Since I just joined this list I don't know of an easy way to reply to the messages sent so far in this thread so I'll say here, I definitely agree with everything in the thread so far; quality suggestions.
For how to have minimized applications available on all workspaces: My first thought was to have a kind of new separate Window List but for icons and basically the same as how the Notification Area is currently used, but if the Design Team wants to get away from that then it limits the options. Perhaps make such a new thing but it is somehow technically strict about what can be done with it; only allow certain responses for left click, double left click, right click, etc. There might be some relevant user interaction studies out there. I will have to this about this.
About removing the workspaces from default installs: Doing so with an alpha or beta would probably get a lot of public discussion going (this is related to the earlier comment about the public not really being aware of 'inner workings' even if they're on a something like a public mailing list) similar to the now infamous window button placement. I use 10 workspaces myself and I recognize I'm definitely not the average user, but I would really prefer if actual releases of Ubuntu still included them so application designers would still keep them in mind even if they only plan to target Ubuntu, for cross-distro compatibility if anything else.
There was that Esfera talk not too long ago and more recently the window button placement, so if Ubuntu is moving into either a more touchscreen-friendly setup by default or more Mac-OS-X-oriented, the suggestions I would make for how to handle a workspace system. But assuming a desktop-oriented usage scenario: I think the Workspace Switcher and workspaces themselves would get a lot more used if moving windows between workspaces was easier. The expo feature in Compiz being enabled by default and popularized in release literature could maybe work towards that. Perhaps a program to do what Compiz expo does but doesn't require Compiz or 3d acceleration could be made for people without capable graphics hardware.
I do recognize that workspaces / virtual desktops are not average user friendly in the sense that the iPhone OS or Chrome / Chromium OS is but even Mac OS X with its reputation for ease still fits in features that probably only more intermediate/advanced people will even use, namely Expose, Spaces and Time Machine. This is probably more than obvious but just to raise the topic, one of the first places I would look is Mac OS X's Spaces since it's the first virtual desktop system to be in wide use by the 'masses'.
Also on the topic of how icons are used, using the right click menu to provide access to mini-controls might be something to look into. I haven't used them but I hear newer versions of Windows 7 and Mac OS X do this. I see it working especially with media players, direct access to controls and all from one click.
Anzan, he might be thinking from the perspective of super-average users, the users that get to facebook by typing "facebook" into Google, I call them the 'masses' (less nicely called the 'unwashed masses' sometimes). I was just thinking about how something like the iPhone might do workspace switching and remembered it's getting mulitasking soon, so that may be a place to look for super-simple workspace switching.