As changing the pairing of lines in four-track areas is slipping into the discussion, I'd suggest grade separated crossovers between fasts and slows on the MML to replace the ladders at Carlton Road, West Hampstead South, Radlett and Harpenden. Clearly putting full twin track flyovers anywhere between the core entry and Cricklewood is not going to be simple, even with unlimited cash. Squeezing in a single track bidirectional flyover taking off/landing between the slows/fasts it would at least avoid most of the contra-flow conflicts, (i.e. up fast & down slow), easing the slotting into correct paths.
It might be more viable if the tracks were paired by direction rather than use, (bit more cash needed there

) making the intermediate crossovers unnecessary in normal service.
The TL/EM working timetable is a work of art, and works well when everything is hunky dory. Random glitches do occur and delays can build making it difficult for the signalling system to feed trains intothe core in the correct order. Generally, it's the EM traffic that takes the delays.