I'm not sure what you mean by substitution class. ? If you mean like
an archetype in Pathfinder, It a little tough to do. ? Making a new
class doesn't really work, as each class has a code, and if you have a
scripted ability, that is based on level you have to go back to all
those abilities and tell them to look at multiple classes. ?
What I did instead is build alternate feat for the alternate class
features. ? In the feat scripting, I told it to remove the feat it is
replacing. ? This is a pain though, as when you level up you have to
choose the new ability manually, and old abilities gets added back
automatically. ? I had to put the removal in the special code so it
would look often and remove it anytime it was added.
Also make sure you feats/class abilities have remove code to undo
anything they did when added otherwise removing them isn't going to
reset the character and you ? may end up with benefits from both.