Bourne End was always going to be a problem.
The "Down" (Marlow) platform is very tight, there's approximately 55m useable length between the stops and the points - not long enough for any currently available AC EMU. There's also little to no possibility of extending the platform at either end, certainly not by the 30+ metres required to operate EMUs
Current musings are to remodel the junction slightly at Bourne End to allow trains off the Marlow branch to access either platform (a layout that existed in the 1960s) to enable trains to "pass" at Bourne End. This would allow a similar morning peak frequency to that currently enjoyed, while continuing to allow Marlow - Paddington to be done with only 1 change post crossrail (albeit at Maidenhead as opposed to Marlow)
Service would operate with 2x 2/165 - a pool of ~8 units based at Reading could then operate Marlows (2), Greenford (1), N Cotswold halts shuttle to Oxford (1-2), Bedwyn stoppers (2) with 1 spare/maintenance. They would join 8-10 3/166 kept to work Basingstokes and North Downs services.
Kennet line service would be re-jigged. Existing 1Kxx Paddington - Bedwyn fasts would terminate at Newbury and be operated by EMUs (likely 387s). Reading Newbury stoppers would extend through to Bedwyn. Kintbury and Hungerford would retain their London through trains by being called at by the Semi-Fast Paddington- Exeter Bo-modes.