What kind of multi-dimensional data are you talkign about? In the R-tree wiki, it states that itis used for indexing multi-dimensional data, but it seems clear that it will be primarily useful for data which is multi-dimensional in the same kind of feature -- i.e. vertical location and horizontal location, longitude and latitude, etc.
If the data is multi-dimensional simply because there are a lot of attributes for the data and it needs to be analyzed along many of these dimensions, then a relational representation is probably best.
The real issue is how do you optimize the relations and indices for the type of queries you need to answer? For this, you need to do some domain analysis beforehand, and some performance analysis after the first iteration, to determine if there are better ways to structure and index your tables.