How is this wiki more confusing to use than wikipedia? Wikipedia uses mediawiki. Our wiki uses a similar way of handling pages as mediawiki does (
http://www.mediawiki.org/wiki/Help:Contents vs.
http://wikkawiki.org/WikkaDocumentation).
Names with two capitals in them are automatically converted to a Wiki link. If you want to use a name like 'Heroes' as a wiki page name you need to add two brackets around it like: [[Heroes]]. It will then be converted to a Wiki link. Page naming is not different in that way. It's just a choice you have to make.
Both mediawiki and wikkawiki use categories. At the moment you have chosen not to use them. It adds the only thing that can be seen as a hierarchy to a wiki. It would be an option to have a category labelled as Gothic3. In that case you can automatically group all pages into the Gothic category. You don't have to use the Gothic3 prefix for all pages then either.
Actually Mediawiki and Wikkawiki are not that different, but if you can explain to me in a bit more detail how in Mediawiki (or wikipedia) things are easier, I'll see if I can change that.
One criteria with respect to the choice of which wiki to use on this site was if I could integrate it. It needed to be 'skinnable' for that and it needed to be in PHP (and using mySQL as database would be nice too). WikkaWiki is a better choice than MediaWiki is in that respect. And it is also a lot faster too.
It is not impossible to install multiple wikka wiki's, but how many would we need? As a compromise we could go with one wiki per subsite of RPGWatch. I don't think we will have too many of those.
That would mean the current wiki will be used for Gothic 3. This does however not solve your problem as when there is an add-on for Gothic 3 or a Gothic 4, you will still need a way to separate them (my choice would be using categories). On the other hand, there is a complete encyclopedia made using only one installed wiki, if they can, why can't we?