The most recent RUS for Kent pointed out that Cannon St & Charing X are now basically at capacity. You can squeeze a bit more out of them with platform extensions, relocking and remodelling but otherwise there's nothing to be done without some painful changes elsewhere (e.g. closing St Johns).
Think the most sensible option is to take the stopping services fanning out SE of Lewisham (Sevenoaks via Orpington, Sevenoaks via Swanley, Gravesend via Bexley) with a portal at Hither Green. This then frees up a lot of capacity at Lewisham and on the approaches to LBG, with the only services being:
Dartford via Greenwich
Slade Green via Lewisham & Woolwich
Slade Green via Lewisham & Bexleyheath
Would also allow the tie-in to a massive rebuild of Lewisham to make it a fit interchange for SE London, taking in:
Bakerloo line extension to Hayes / Beckenham Junction
DLR extension to Bromley North
Direct covered bus interchange
On the other side of London, the sensible place would seem to be the lower end of the WCML, given the development opportunities up the far end where housing density is very low and connections into central London are poor. I'd have thought taking over the WCML slows from Willesden Junction north would give a reasonable level of service, calling Willesden Junc, Wembley Central, Harrow & Wealdstone, Hatch End, Bushey, Watford Junc & all stations to MK Central / St Albans Abbey.
Central London route would need to look at relieving the Jubilee / Bakerloo lines. A Kilburn station connecting Kilburn, Kilburn High Rd & Kilburn Park would help development in NW, Baker Street is an obvious calling point as is TCR. From there I think you'd want to go to Charing X and then into SE London through E&C and Peckham, as these are the target growth areas in South London.
On a separate note, Crossrail 2 should take over the ECML slows north of Ally Pally through to Stevenage via Welwyn, with the NCL having the same via Hertford. The semi-fasts off of STP/KGX then call Finsbury Park & Stevenage only meaning they can run on the fasts in between.