How malleable is the Bitcoin protocol?
The number of Bitcoins in circulation


That would be almost impossible to change and would drastically undermine confidence in the Bitcoin system. I think we're stuck with this forever, or until Bitcoin becomes obsolete.


  The rate of Bitcoin production


Again, almost impossible to change.


  Or the number of confirmations before a transaction is confirmed?


Anyone is welcome to consider a transaction confirmed after as many or as few confirmations as they like. There is no reason this requires any kind of agreement.