There is a proposal to allow the inclusion of Java applets into Wikipedia to increase interactivity. What this says to me is that the Web is not enough and that it is mainly a document system. Instead, the Wikipedians should build a proper desktop application for viewing Wikipedia articles and then separate it from the Web and HTML. This would allow them to display the information in a variety of forms and fix the flaws of the Web.
The first thing I would add is a way of linking to specific paragraphs or sentences. The second thing I would add is a proper discussion board system and possibly add an IRC chat component. For the chat component, I would also make it easy to paste snippets of the conversations into the discussion board. This is useful because you may have discussed an article with someone and then made changes to it, but everyone else would be unaware of your discussion unless they checked the discussion board and the discussion may have provided a rationale for why you made the change.
Java applets and more interactivity would be a fine addition to Wikipedia, but this is solving the wrong problem.