Let's say i have a cube and a cylinder as a reference. I create a small sphere, i put it inside a cloner and as a clone method i choose OBJECT. in the object tab, i put my cube. So the spheres cover the cube shape.
Now i keyframe the object tab of the cloner, then I go 25 frames more, i change CUBE in the object tab with CYLINDER and i keyframe it. So the small cloned spheres moves from cube shape to cylinder shape. The problem is that i would like to have a smooth animation of that.
use an Inheritance effector instead. To do that kind of thing the usual method is to clone onto cube as normal then use a Matrix object with the cylinder, in Object mode like the cube, which will apply little matrix cubes in the viewport to show you where the objects will go but they don't render.
Next apply an Inheritance effector to the Cloner, with Inheritance Mode = Direct (the default) and Morph Motion Object checked and drag the Matrix object into the Object slot. That will automatically move all the clones to the cylinder. You can control the sphere's movement from the cube to the cylinder via the Strength slider in the effector or use a falloff with the effector and animate that.