Entry codes
The way I see it, the system needs to cater for the following:
1) Prevent unauthorised access to the flight deck
2) Give access to flight deck in emergency such as incapacitation of both pilots
3) Access to flight deck by person who SHOULD HAVE ACCESS - the pilots!
Point 1 and 2 are already catered for by the current system. Which leave us with point 3, highlighted by recent events. To overcome this, before the flight each member of the flight deck sets a personal code that will give them access to enter. A bit like setting the code on a safe in a hotel room.
Whereas the code that gives access to authorised cabin crew (emergency point 2) does not have the power to override the Manual lock (set by the flight crew -current functionality), the individual flight crew member code does.
This ensures that neither of the flight crew can 'lock' the other out of the cockpit whilst at the same time maintaining the current functionality.
I hope that makes some sense