I like the theme mockup Brahim. I would change the Scrollbar though... either to a green version of the older Aqua one from Tiger I think, or the Flat version you already use just colored to complement the overall color of your theme.
Now on to the main thrust of this post:
Your Theme Manager idea is in fact pretty much the same as mine, though I would have went with this base design http://fc06.deviantart.net/fs70/f/2013/255/a/1/control_panel___theme_manager_by_hexdef101-d6jkrse.png
thats the old control panel mockup I made (and never really finished) but its applicable. Beleave it or not Cinnamon Settings Is good enough that I wouldn't really change it... even to completely match my overall design. I would just add some sub categories for better customization of the desktop.
Themes: Thats surprisingly exactly My Idea. I would in fact go with the pre-built Os themes, though I would also add KDE Plasma to the list (overall design at least). I would do one thing slightly different though. I would Categorize the themes by Vender (Linux,Microsoft,OsX,MacOs), And have pull down menu's for the version of said theme. Using Microsoft as an example (want to be fair
) have a pulldown with Classic (95,98,2000), Xp, Vista, and 7.
of course There is the color Issue. I would Create those themes with the ability change colors. Taking Xp's Luna theme. set it up so that its color is controlled separately and system-wide. this way if you wanted a red version of Luna all you would have to do is change the Theme Color. Gnome had a couple of themes that sorta did that but they were not system wide, so Metacity Wouldn't always match. A Blue Leopard theme, yep we can do that.
Controls: I would in fact go with a separate theme style for these. it would be fun to have Microsoft 7's air theme with Os X Buttons and Controls (in the colors of the Air theme of course). I know Emerald Sorta did this (never could get it working on my system though).
Hybred Desktop: yes Though I wouldn't necessarily go as far as matching the control scheme's of Android,IOS,Or that travesty Windows 8. My Idea is to take the the dock and Turn it into a menu system. The subcategories Look like the Slide Window in Cairo Dock like this http://imageshack.us/a/img40/2327/20189111.png
As you can see it takes the Dock and puts it back in its proper place (as a Over Glorified Menu). I Use a Gnome 2.0/Os X placement though you could reverse that easily. User Controlled. (oops just noticed the wrong menu is highlighted in that mockup
Xtra Credits: Yes I wouldn't mind a Theme in the Default Colors of the Forum (those can be changed btw, or can in other forums with this system). in fact I would have preset color schemes in my design for overall system colors anyway, so this would be a moot issue. But in the interim I wouldn't mind seeing one. A green version of Nord or Tout would be interesting.
Also I know I used the original OsX dock shape from Tiger... I did that because it would fit the old Gnome 2/Unity Design, and would work inverted to the Linux/Windows desktop setup. a 3D dock never looks right on the top or sides to me. That one at least would
As for Universal Menu's on the Panel Like Apple. I do Like them, Never seen them done Correctly though, Not even by Apple (and they designed it, though at least it does work) Ubuntu kinda messed the design up. Though I do use the version for Cinnamon (just to have them there). And the Panel Logo/Menu I would make that System Admin stuff (About this Computer,etc). The "Finder" Icon User Menu (User Icon, About Me, and Lock/Logout/Shutdown) I am big on having as little redundancy as possible (understand the reason, just don't like it)