There seems to be some considerable mis-understandings around concerning the content and significance of Control Period 6.
From CP6 onwards the settlement between Network Rail and the DfT (and therefore the Treasury) for funding will cover
only the on-going costs of operating the railway - that is operations (signalling and so on), track and other infrastructure maintenance and 'like-for-like' renewals and replacements.
The CP6 settlement does
not include funding for any enhancements to the network - that is electrification, adding tracks or building flyovers and the like. These will be designed, costed and, it is to be hoped, the capital expenditure will be approved by the DfT on a case by case basis. This returns the process to that followed in the days of British Railways.
There is
no shopping list for CP6. All that 'deferred to CP6' means is that the project will be approved/started/completed (delete as appropriate) during the CP6 period, that is from 2019 to 2024.
Or might TfL take over all [passenger] services on the relief lines Reading - Paddington, leaving GWR to provide Oxford-Didcot-Reading stoppers?
Anything is possible. However the published current plan is that the two stopping trains per hour between Didcot and Reading will continue to (and from) Paddington making a limited number of stops at Twyford, Maidenhead, Slough and (IIRC) Hayes and Ealing Broadway. When these were formed of Class 165/166 trains they started from and ran through to Oxford, which of course is now impossible as the wires end at Didcot. In view of the considerable traffic which runs through Reading, Maidenhead and Slough being considerable employment centres, it does not really make sense to force these passengers to change. Especially into what is, in effect, a Tube train.