It would be very helpful to have namespaces--think of it as a folder structure. While categories allow you to group pages on similar topics, the advantage of namespaces is that they allow you to have pages that are named the same but which fall into different section of your wiki. It's very easy to wind up with duplicate page names unless you make all your page names very long and descriptive.
Namespaces could use a convention such as [[namespace:page]]. They could be nested [[namespace:namespace:page]].
When creating links for new pages, those links would automatically be assigned the namespace of their parent page, unless the user specifies a namespace in the link. Ie, if you're in the namespace "projects", then a link on one of those pages would automatically become [[projects:newpage]].
Implementing this will also make it easier to possibly implement access control restrictions by namespace in the future. This could allow, for example, a user to have part of their wiki be private (by having a namespace that is only accessible to them), and part public, or for certain departments in a company to share the same wiki but only have access to certain parts.
In fact, for simplicity, the 'private' namespace could be build-in to Instiki, so that any user who uses that namespace will automatically have it visible only to them without having to set any access control settings.
