I would rather have e-mail notifications on by default for new users.
Most people do not like to read several paragraphs explaining out to do this and that. For example, my students sometimes are surprised because they didn't know about some warnings delivered several days ago. I know they could use the feed button to get timely information delivered to their feeds reader, but probably most of them do not have a feeds reader or do not know what that is. Or, maybe like me, never got used to use a feeds reader.
So, when I want to be sure everybody gets informed about some urgent issues, I use the newsletter feature (great tool, by the way!).
So, I would go for e-mail notifications on for new users by default. If possible, for all activities (so that my students would not miss a new warning: at the moment, I have to duplicate efforts: send a newsletter and also writing in the forum). With any e-mail notification there could be a short bottom line explaining how to change the settings of e-mail notifications, so that the knowledgeable person can change it as better fits their needs.
If such a option is not appropriate for other sites, then the next best option would be to give the manager of each specific wikidot site the power to enforce that every new member of that site would have e-mail notifications on by default (and maybe even with the possibility of preventing members to disallow such a feature).
Another thing that would be nice for private sites would be the possibility of seeing, in the profile of each member, what activities he has done, at least the ones related to that specific site. At the moment that is not possible when the site is private. As you can imagine, this would be a big improvement when a site is used for education matters. Or try in some way to get such a feature within the new Activities tab?… But then old activities should not automatically disapear (and maybe would not be the right place for a site with more than 400 members!).