it morphs clones of one single cloner to another cloner's shape (could be Linear, Grid, Object - doesn't matter) so you are always going to be using the original clones from the first cloner.
So, you have to deal with the material on the clones - you can change the material by keyframing the Texture tag on the clones.
There's a color change on the clones at the end of this example.
4419_inheritancemorphtest.c4d.zip
it uses a poly with a single vertex as the clone since that's the most efficient/quickest thing to use with a Metaball so the material is on the metaball not the cloner itself