What is the total cost of patenting a medical device in Europe?
Cost of Filing Patent change from time to time, at present cost of filing application can be found at following EP interactive tool:-
Schedule of Fees
Then selecting the Fee Group based on your requirement.
For your reference filing a application and related cost on various matter will be as follows:-

Please note that these fees are official fees and does not involve attorney costs.
In normal course as fresh filing You need to provide fee for CODE 1 (only one online or physical filing), 2 and 5. if claims are more than 15 additional fee as CODE 15; If certified copy is to be provided then code 29; if page exceeds 36 CODE 501; and if divisional is filed CODE 552-555 based on applicability.
I have also heard that the cost will significantly reduce with a new
system. Is that already in place? If not, will it be in place any time
soon?
At present No fee changes notification are given and most likely they wont change in recent time.