Unfortunately impossible things that would improve Sub Surface Line capacity:
Reaarange Baker Street Met platforms to be like Aldgate and Edgeware Road with the terminating platforms in the middle
Grade separate Baker Street junction
Grade separate the Aldgate/Aldgate East/Minories junction triangle
Grade separate and rearrange to have terminating trains in the middle at High Street Kensington
Grade separate Gloucester Road junction
Grade separate Praed Street junction
Bonus points if your multi-billion pound rebuilding project under protected buildings and congested streets can furnish the terminating points with reversing sidings for optimum capacity and to make things simpler for passengers
Automatic train operation run by computer, centrally, will solve a lot of problems without having to rearrange junctions. The computer always knows where each train is, so if one train is late, it can work on the network as a whole to slow things down or speed things up so paths still 'slot in' properly at flat junctions.
Although it's now going to be 2021 to 2023 before the resignalling is finished, once it has, they will be looking to run 32 tph between Baker Street and Liverpool Street, compared to 27/28tph at the moment, so around 20% extra. It may even be possible to go up to 34 or 36 tph (like the Victoria Line) but this is where it starts to get more difficult with the Circle/Met/H&C as it does take some time to get over a flat junction.
That said, if the computer can time things to the second, who knows.