I'm not sure I follow. Why would a subclass even need to fundamentally alter the base class so much that it no longer plays like the base class?
Let's say you have only four classes: Warrior ('martial focus'), Sneak ('skill focus'), Mage ('full caster'), and Priest ('half caster.'). These are the chassis that you will build your character concept on.
Now let's say that out of ten dozen different subclasses, you decide to go with Acrobat (the first one that came to mind, but it could be anything). If you choose the Warrior class, your Acrobat would be a martial focus and would feel more like a swashbuckler or skirmisher...but if you chose the Sneak class, your Acrobat would be more like a catburglar or ninja. If you chose the Mage or the Priest class, it would gain the appropriate amount of magical talent, making it feel more like a shadowdancer or assassin, or something entirely new.