Personally speaking I'd re-build Welwyn Garden such that the Flyover works 'the other way' taking trains over towards the Up Side where stabling could be created. You'd only then need a 'Down ECML' Platform, two through roads, an 'Up ECML Platform', and an island next to that for the Crossrail 2 stuff.
You could legitimately suggest a combination of 'semi-fast' and 'slow' Welwyn trains for Crossrail 2 such that Thameslink services could all operate fast from Finsbury Park to Welwyn in either direction using a new higher-speed crossover on the down, with a 3 minute stop each way to let a Main Line train overtake and then they follow them out; meaning Welwyn still got a fast Thameslink connection and the Cambridge trains could be accelerated.
In terms of other interventions, I'd suggest turning the US2/US and DS/DS2 platforms at Harringay, Hornsey and Alexandra Palace into islands in each direction and with the through lines then without platform faces; and you could then use the DS and US as 'accelerating' or 'decelerating' lines as far as about the end of the Hornsey Depot (north end) with a DS>DF and UF>US 75mph crossover and 60mph line speeds from Hornsey platforms to Holloway so the main line is a bit less cluttered there with slow turn-outs at Finsbury Park north end. It also creates more flexibility if a train goes 'demic' in one of the platforms and stations still get served.
I'd therefore go for 16tph out of Moorgate using the 717s but with 8tph to Gordon Hill, 4tph to Hertford North and 4tph to Stevenage; the Gordon Hill bay platforms then being put in the 'middle' so as to remove crossing conflict (think Dalston Junction) and then trains being routed round the outsides if travelling through. It would also be the case that some trains (assuming they operate every 3-4 minutes) would miss out the smaller stations (Hertford and Stevenage trains not stopping at Harringay or Hornsey; Gordon Hill trains missing out Grange Park and Stevenage trains missing out Crews Hill and Bayford).
I would effectively push Crossrail 2 to be something like:
-CENTRAL CORE Dalston (Junction and Kingsland) > Essex Road > Kings Cross/St Pancras > Tottenham Court Road > Green Park > Victoria > Clapham Junction > Tooting Broadway > Wimbledon > Raynes Park.
-NORTH BRANCH Welwyn Garden > Hatfield > stations to Alexandra Palace > Hornsey > Harringay > Finsbury Park > Dalston
-EAST BRANCH Chingford > stations to Walthamstow Central > St James Street > Stoke Newington > Dalston
And whilst Raynes Park would be underground (junctions towards Epsom, and another that climbs up to join the Main Line before New Malden), it would be the last point in tunnel before opening out. Assuming peak frequency of 24tph from the Crossrail 2 Core (8tph Chingford, 12tph Welwyn and 4tph Dalston starter), you would have 4tph to Horsham, 4tph to Guildford via Epsom, 4tph terminating at Epsom, 4tph to Chessington South, 4tph to Hampton Court and 4tph to Guildford via Cobham. This would leave the Kingston Loop and Woking trains as Waterloo starters but each would be 4tph (extended Woking to Guildford assuming the flyover is built) and credence given to double-deck trains to provide the necessary capacity.