The same behavior occurs in 9.3.1, 10.0, and 10.2... that is, you cannot register a feature class as versioned within a feature dataset but not register the other feature classes within that same feature dataset. If you only want to register a single feature class as versioned, you will need to consider moving it out of the feature dataset. However, if you do that then the feature class can't participate in things like geometric networks, parcel fabrics, or topologies.
As for the first part of your post, I'm not sure if this is your production database or how much data you have, but might it be possible to create new feature datasets and feature classes... then load those feature classes with the data from your existing feature classes? Otherwise, it may be cleaner to simply create a new geodatabase entirely... although more time consuming.