Hey koji,
Recently I used zf command(zf.sh), but it's hard to use.
I guess you mean that it doesn't have all the features you'd like :)
I think that usually something like controller class have their parent class custmized for each project or company. But the class files generated from zf command extend Zend_Controller_Action. I need to fix it. Form and DbTable are as well.
It does lack some project specific customizations, this is on the TODO. See my full list in the response to Jurian.
I think there is no need to use zf command. I'm using code generator I made. It has customizable skelton file.
You should have a look at Zend_CodeGenerator. THis is a stand alone component that does non-template generation of object oriented assets like files/classes/methods&properties/etc.
It might reduce the amount of work in your toolset. -ralph