The SWR Table 149 probably needs to be taken with a pinch of salt as it conflicts with the draft, and heavily revised, GWR timetable for the North Downs Line currently showing on NRE effective from May. Example:-
A SWR service from Waterloo leaves Wokingham at 13:19 and arrives in Reading at 13:32.
Meanwhile a GWR service from Redhill arrives in Wokingham at 13:21 and overtakes the SWR service on a soon to be built flyover south of Earley to arrive in Reading at 13:31 ....
It also only shows four trains per hour calling at Queenstown Road (Hounslow Loop trains still calling there, but not Kingston Loop or Hounslow via Richmond), whereas SWR is now saying it will retain eight trains per hour here at least until the completion of the Northern Line extension.
SWR is also now saying it will retain the direct Waterloo-Weybridge via Hounslow service but at the expense of its proposed four trains per hour to Windsor & Eton (two via Richmond, two via Hounslow) so the W&E branch will now remain half-hourly at least in the off-peak.
The consultation outcome report on the SWR website also mentions additional calls at Vauxhall on some morning peak trains from Reading - this is not shown in this draft timetable (which was presumably done before the consultation). At present, Reading trains call at Vauxhall on Sundays only, and even that is a fairly recent thing.
AFAIK there are no plans for any significant changes to weekend services on the suburban routes or the Windsor and Reading lines.
I didn't know there were plans for a new flyover near Earley - that's news to me. In any case, even if it were true, surely it would be west not south of Earley, as the Waterloo-Reading line heads in a north-westerly direction between Wokingham and Reading.