I'd leave the network more or less where it is.
Except I'd stick it all underground. And make all junctions grade separate.
And add an extra pair of tracks to the Circle, running Circle services as high frequency stopping at all stations and the other SSR services as express.
on the GEML and GWML I'd create an extra pair of tracks for Crossrail throughout (and two more tracks up the GEML to Ipswich for local services)
on the ECML I'd add two extra tracks to Welwyn Garden City for Moorgate services.
On which, the Hertford loop services would gain their Stevenage terminus facility.
And further to this, they'd become Crossrail 3, with services running through to meet the Bexley, Bexleyheath and Abbey Wood routes. A third "north" branch would be short, following the old route to Alexandra Palace via Highgate. The Crossrail 2 western arm would not terminate at Southgate, instead also running to Welwyn Garden City.
Assuming the Hayes branch would get taken over by the Bakerloo.
I'd do the Watford DC-NLL thong, supported by an Outer London Freight Orbital. The New Cross branch would go to Bromley North and the Bakerloo northern end would head west into untouched territory
Acton to Rayners Lane would go to the District Line but using Met Line S8 stock.
Two extra Thameslink tracks for Thameslink Metro (rebranded Crossrail 4), which as well as Sutton loop would taken the remaining Southeastern metro lines.
Much of SW Metro would have been dealt with by Crossrail 2.
the reamining Windsor side SW metro and the bulk of the south central metro would be a problem. South central especially, it's a tangle of low frequency services at the moment. Any rationalisation means people would have to change trains more.
Important: All Underground, Overground, Crossrail would have platforms (re)built to be straight and level with level boarding and step free access to the street.