The question you seem to be asking is "How can I make my UI skinnable" which is completely independent of any kind of technology for representing those choices.
If you want to built an HTML based application, then you can either have a UIWebView or develop a web-based application, both of which can be skinned with CSS.
If you want to make a UIKit application customisable (by changing background colours etc. and the like) then you'll have to roll your own way of doing that. CSS would be overkill for this purpose, and in any case, there is no 'standard' support for themeing applications. You might as well just write into the user defaults (probably via a settings bundle) what the user would prefer as a background colour etc. and then write a method to traverse your UIKit hierarchy to change the background colour as appropriate.