If you have to start from scratch, what principles and features should be embodied by a new wiki:
Openness
Within limits since newcomers don't need the ability to delete paragraphs, merge paragraphs, delete pages, create more than 10 pages a day, and so on and so forth.
Automation
There shouldn't be a need for human intervention in routine activities such as creating a newcomer account.
Reflection
Privileges of the wiki's users should be accessible and modifiable in the same way as any other content of the wiki.
Security
The ability to restrain bullies, to close off pages to everyone but selected participants, to have any grain, any permutation, and any kind of legitimate collaboration imaginable.
Responsibility
Your signature gets attached to every edit you make, deleting signatures is a completely separate privilege. Privileges are managed by human beings and can be revoked. Management of a group of users' privileges is itself a privilege which can be revoked.
Would RealNamesPlease apply, or could one be an AnonymousCoward or use a pseudoynm?
Non-linearity
Though this would be extremely difficult to implement within the limitations of the web.
Please explain what non-linearity means in this context.
Wiki links make the wiki as a whole highly non-linear; hypertext instead of text. However, the pages themselves are highly linear and people must spend an inordinate amount of effort on demarcating their non-linearity when they wish them to be so (ie, to distinguish threads and speakers). Basically, the grain of non-linearity (the page) is much, much too big.