The popup is doable, the mobile version works kind of that way. There is also the download, apply filter and edit with pixlr area that would make it open another popup or change screens. I need to think if it worth the change.
I can agree that a bigger skin chooser is better, but the most used option is to select a skin file from your computer instead of picking one from the gallery.
The mobile version has an unobtrusive skin chooser, we can try to make something similar. But, is the balloon that shows when you click the player a bad thing?
Moving the author profile to a more visible area is easy.
Loading wallpaper thumbnails as you scroll down the page, done.
Collaborative resource packs, doable with Dropbox I think, but it will require lots of work to implement. Planned for the future.
The badges of the forum. I don’t control it, I’m just using http://discourse.org default settings.