The big plan they had was to instigate TCAS (Train Communication And Signalling) that would allow a higher flow rate through the network. (Instead of signals controlling blocks of track, TCAS would just maintain separation) This was being rolled out before I left, roughly 5 years ago. You can probably thank the militant arm of the RTBU (drivers) for that little gem.
Anyway, regardless of that, the City Loop, as cattletruck mentioned, is the achilles heel of the system. Honestly, I don't know of anywhere in the world where trains reverse direction in a tube/loop at lunchtime!