I think it would be nice to add an apply method to the tree. Currently there is one in the RandomForest, but not in the tree. There is one in tree.tree_, but the tree object is not publicly documented. I think the idea was that we might want to change the structure of the tree object, so we don't make it public.
Still we could provide a public interface to the lower level functions so that people might find them more easily.

Opinions?