I agree with removal of freight and simplification.
The best thing for the GEML, NLL and others would be some sort of dedicated freight line from Anglia (entry from both Felixstowe and Thames Riverside/Tilbury way) - meandering through the country to hit the MML somewhere south of Leicester and of course, get to Nuneaton another way also. Inland Rail in Australia - Shires-style!
I would rebuild Willesden Junction Low level as two islands (four faces) - with the inner ones turning back either additional Stratford services, or the many more Bakerloos to come, if extended to Lewisham/Hayes. I'm less concerned about Willesden Junction WCML platforms - but it's a good terminus for metro frequency.
WLL - someone invest in the platform zero at Clapham Junction - and up the WLL/SLL frequencies accordingly. 2tph WLL Overground run up to Watford P10 instead (semi fast still, they'd keep time north of Wembley) - and the Southern service goes away. I'm sure that path through South London and Windmill could be better used - even as a 1tph to Victoria extra.
Beyond LO - the GN Moorgate route needs to also be taken seriously as a metro. No outer London calls anymore (Potters Bar even goes 3-4 trains peak direction only) - but replaced with 6tph Welwyn GC and 6tph Hertford (2-3tph Stevenage) minimum. Clock-face - some could skip Harringay/Hornsey but otherwise all stations. CR2 doesn't need to go that way either, pointless.
I have lots more thoughts - obvious one is all TL services terminating at Kentish Town/WH run on to St Albans at least. I'd build a fast tunnel / dive-under running under St Albans too for MML services - enabling more use of all platforms for services to call / turn.
Watford Junction - bigger beast to wrangle but I'd try build another platform on the eastern side to give a bay, and make P10 up slow, with 9 as a middle bi-di road. 11 for other terminating services, and a new one p12 for Flyer.
Wholeheartedly agree with moving freight out of London Z2/3. My ideal would be an orbital route paralleling the M25, but I'd settle for a deep freight tunnel from Ripple Lane to Wembley (and maybe on to Acton). Freight means no stations, no stations means you can go deeper, and electric freight means ventilation is easier; only real concern is gradients up to the yards.
Willesden Junction, yes. I want slow line WCML platforms, though, and platforms on the WLL lines. They're needed for making the most of all the interchange possibilities.
Clapham Junction, yes for 0. I wonder if there's a case for extending west from Clapham Junction, perhaps taking over the service via the Hounslow loop to simplify the SW routes, though what you would do at the end is a bit spicy.
MML fast line tunnel at St Albans is seemingly a no-brainer, but I suspect the real solution is HS2 to East Midlands Parkway to free up paths for more slower services, which wouldn't need the tunnel.
...and finally Watford Junction. Good ol' Watford Junction. In no particular order, ideally we would bury the Abbey Line deep (steps down to new platforms from the existing subway deep!) under its original alignment around the north of the current car park, run under Orphanage Road, then pop up to join the DC lines just north of Radlett Rd (or, if the gradient is too severe, then Radlett road converted into a bridge over the new, lower, railway).
Unlike St Albans, Watford Junction can benefit from HS2 capacity, so I'd like the 9/10 platform rebuilt as an island. Ideally we'd get another island built east of that one (so everything could shuffle over and the fast lines could have 4 platforms), but I suspect that's not possible, curvature-wise. I'd like platform 5 reinstated, with platforms 5&6 used for the fast services. Platforms 7&8 then become a northbound slow island, and platforms 9&10 become a southbound slow island, with 8&9 bidi for turning services from either direction, as required.
