I'd posit that these smug systems may have resulted from use cases, and traditional user-centred design. We've been taught to design systems for a purpose - preferably one purpose - collected through use cases and designed against them. Use case collection never really includes crazy ideas or tries to foretell unexpected and unplanned uses. Good design, in my mind, is designing enablers or tools that include the use cases given, but have breathing room, rather than designing strictly to the use cases. It could be said that this reduces usability, and it often does, but with the flipside of user value.
On digital marks of wear and tear:
Argh. No. This isn't digital art. And again, it's unnatural given the situation. If we have wear marks, we should really use the metaphor of real paper, and real books. The natural marks of electronic text are the links to, the referrers, the views, the links out: the hypertext, the associations, and the metadata. These can be visualised to provide implicit signals.
On IDEO and design science:
Any attempt at providing the "science bit" only works if you have great designers who know when to break the rules (this is the sleight-of-hand that IDEO play - provide a seemingly rigourous process to pacify management, then use designers who don't need to follow the process to produce good results).