Passives already have two levels in the game and i propose to keep the same (or similar) overall numbers but split this up into three levels instead called focus.
then when you build your class or subclass you can only access the level that you have in active class skill lines. So if you have 3 same class skill lines you can access the full passives. If you have two of the same class skill lines you can access level 2 ( for the two same class lines you have) and if you have three different skill lines you can access level 1.
This provides some basic balancing of subclasses while preserving the original classes. So the original classes have the strongest overall class passives but the subclasses have the best synergy potential and flexibility. I believe this is a good compromise for initial balance, makes sense, and is pretty easy to implement since its kind of already in place for the most part.