Like others have said, you should provide more details on your configuration and your goals.
Sticking with the git-subtree solution (assuming it's indeed a good solution, and I can't say for sure), you can try creating only one external repo, containing ALL your assets, and include that as the only subtree in the main project. Having only one subtree keeps the complexity down, and you can keep your skins history separated. In the end it's likely that, when you have to change an asset, you have to do for all the skins, or you end up with inconsistencies in your layout. For this reason having a separate repo for every skin is overkill IMO.
Additional tip: if you're working on a Mac (I hope you do so ;) you can give a try to Atlassian SourceTree, a free git GUI client that recently introduced support for git-subtree. I don't like GUIs very much, but I found this one very handy when managing complex subtrees setup.. There's also a Win version, but it doesn't contain subtree support yet (it will soon).
Hope this helps..