Why the hell didn't Visser One give himself (as in his yeerk body) the morphing power, as soon as he got the cube? He's a megalomaniacal, power-hungry sociopath, so you'd think he would use it to strengthen himself right away.
However, for some reason, he didn't seem to do so, even though Tom's yeerk was morph capable.
That would have caused a few problems in confining him, I think.