The E was always inapprpriate and probably instituted by DIRD/CASA and Airservices to bring disrepute on the class of airspace.
Class D under tower control would have enabled use by smaller aircraft but positioned by the controllers where they did not impede the departure and arrival of IFR aircraft.
Unfortunately Airservices operates it as though it was a high volume airport such as Tulla, when in fact it is quieter than Moorabbin on the other side of the bay. This means that radar control will continue even though it is very inefficient for such aerodromes.
This is probably because the Melbourne Centre ATC chiefs have very little experience with Class D airports, unlike Brisbane Centre where they operate with four Class Ds and 2 Class Cs.