The problem is Marlow passengers have got used to the through service to Maidenhead, so enforcing an additional change for short local journeys would be very unpopular, and might have unintended consequences on branch ridership especially leisure and off-peak during the day. The Henley and Bourne End direct London trains have always been difficult to justify from a capacity point of view, but politically they're impossible to curtail, at least today before Crossrail is established. Once that is up and running, I'm sure a single change a Maidenhead for a range of Central London destinations will be just as attractive as the though train to Paddington, where most passengers change for onward travel.
I was implying that removing through trains was something for when Crossrail was operating. It might be unpopular with the voiciferous commuter groups but as you say the improvements from Maidenhead more than make up for it. There should be guaranteed seats on Crossrail at Maidenhead.
