Interesting...I did test it and was able to get it work consistently so my guess is there is something amiss with your query (although, typically you would get an error, not all results returned). Is your lowest level portfolio item type called "Feature"? And Initiative is your second level?
I tend to use the wsapi doc to see the full object model: https://rally1.rallydev.com/slm/doc/webservice/
You can use dot notation to query attributes of related objects, e.g. Feature is an attribute of "HierarchicalRequirement" which is the object name for a user story, and feature is itself an object with attributes so for stories you can do queries on attributes such as Feature.Name, Feature.FormattedID. And remember that objects inherit attributes from their parent so you can use those attributes too.
The data model gets interesting with Portfolio Items since you can define your own portfolio item hierarchy and query each separately. I was actually surprised that PortfolioItem.Parent worked in the story query but happy to know that it did (I learned something new!).