I'd be interested to hear about the plans for the Thames Branches. DMUs are going to be required for Reading - Gatwick, Reading - Basingstoke, north of Oxford and west of Newbury (although the latter two could be provided by stops/additional long-distance services), so keeping hold of extra DMUs wouldn't be too much of a problem, except for the direct trains to/from Paddington (1 train per weekday Bourne End - Paddington; 2/3 trains per weekday Henley - Bourne End) but of which there are so few would probably not be too hard to curtail at Twyford/Maidenhead. AIUI there is also a separate plan as part of Crossrail to terminate Greenford trains at West Ealing. On the other hand I expect that electrification of Marlow/Bourne End and Henley branches could be done quite cheaply as part of the total project.
Personally I think that Slough-Windsor should be electrified & become part of Crossrail (though it may require a flyover to access the slow lines at Slough), considering that Windsor has a large tourist market as well as commuters
