I don't hold with the given reasons for APD, but
if there's to be an "environmental" excuse it would seem reasonable to raise the seat-capacity threshold a little, say to 50 or 70 seats. This would effectively exempt the supposedly cleaner, less damaging turbo-props and would/might encourage more use of regional airports, either delivering passengers into a major hub for their holiday flights or with low-frequency direct flights to "business" destinations.
A correlation with passenger numbers would also be beneficial, helping to slow down an airport's growth as it nears saturation and conveniently avoiding the need for second or third runways = happy ecofolk!
The airlines would then have an incentive to build up services from "underused" airports and individual airports (and local authorities) would have an incentive to invest in a quality "passenger experience", including the interface with other modes of transport.
I missed the deadline for contributions to the reform consultation.