I just noticed pcl has a couple of duplicated readers and writers for some file types, e.g. PLY and OBJ, in which one is normally a full reader/writer implementation made in pcl and the other one invokes VTK readers/writers.
For the PLY file format I think it is intended to provide more functionnality than the VTK PLY reader/writer:
the PCL one allows to write intensity etc... the vtkPLYReader does only support red, green, blue:
So, assuming the idea was to the extend the reader/writer's functionalities, I imagine that idea would also imply at some point to phase out/deprecate vtk's readers/writers. This make even more sense if one takes into account that vtk is an optional dependency.