This was one of the gripes we had with indentation in CKEditor 3.x/4.0: the fact that you could indent pretty much anything, rather than just HTML tags that actually allow for nesting.
E.g. it was possible to "indent" paragraphs, this would just add style attributes with a LTR margin. That is very much against structured content principles.
All we have to do to fix this, is when we update to CKEditor 4.2, we must update our build-config.js file. The indent plugin has been split up into the indent (providing core functionality), indentlist (indenting for lists, i.e. <ul> and <ol>) and indentblock (indenting for paragraphs et al.).
That means we can update our build-config.js to just include indentlist where it currently says indent. CKBuilder will automatically pull in dependencies.
