The Switcher in Windows 8 is really convenient for managing running applications, but unfortunately all desktop apps are grouped into one position in the switcher... I like to kill background apps with the middle mouse button, but it's not possible to do with the regular "alt-tab" switcher... Is there any way to have the best of these two worlds - that is the ability to easily kill apps with the middle mouse button but without desktop apps being grouped into one item?
There are two ways to switch between applications win+tab and alt+tab.
Using win+tab all Windows 8 Store apps running are shown individually in the left task switcher. Desktop applications in this scenario are all shown as a single block - "desktop". There is no way to show them individually with win+tab.
Using alt+tab all Windows 8 Store apps running are shown individually in the center task selector. Desktop applications are ALSO shown individually and the user can alt+tab and shift+alt+tab through them as desired.
This is how it works. win+tab simply groups desktop applications like it or not. If you don't like it (and I can understand why not) then use alt+tab (which is the old standby anyway).
Bonus! There is a third way, of course, to switch between applications either swiping from the right with your finger or pointing your mouse to the top-left corner. But I think it was keyboard shortcuts you are really asking about in your question.
Alt + Tab shortcut toggles between each active Modern UI (formerly "Metro") app and desktop app. This is what you want. Win + Tab shortcut will toggle between Modern UI apps and your desktop only, which is not what you want.
As far as closing apps via clicking the mouse wheel, you might want to try Microsoft Mouse and Keyboard Center for Windows 8 to solve your problem. You can download it free from Microsoft website.
Make sure to choose the right version for your computer.
Once installed, if you have a supported mouse, then the app should detect the device. Here is a list of supported mice.
If your device is detected, then you're all set! Just use MS Mouse and Keyboard Center to reconfigure the behavior triggered when clicking the wheel to close apps. For directions to change settings, search on Microsoft for "Windows 8 How-To: Mice" (I would post the link but I'm only allows to post two links max).
It reads: "Customize basic settings for your device. Your Microsoft device comes with preset button and key settings. You can reassign them to different commands or keyboard shortcuts that better fit your work style. You can also disable buttons you might press accidentally, such as the wheel button.
Reassign a button or key
(My mouse is not supported, so unfortunately I could not complete testing this resolution. Hope this helps.)