I believe that changes to minor mods will come in when the EASA scheme of charges comes into force. These charges are expected to be introduced during the summer at which point it will be illegal for the CAA to charge for the parts of the EASA regulations that EASA are directly responsible for, i.e. design and certification tasks. C of A issue, etc stays with the CAA as this is delegated to the competent authority.
It is still a bit sketchy, but I believe the basis process is that minor mods for aircraft over 2000kg will be done directly by EASA (no CAA involvement) and we will have to pay EASA directly. For aircraft under 2000kg these will be done by the CAA at NO CHARGE!
As has been said all approvals of STC's must be made by the holder directly to EASA/National Authority responsible for the type. This is basically because the FAA deems an STC to be a major mod.
ACX