Looks like Crossrail is meant to at least partially address the Chelney route(s).
Some of those new stations are getting rather ridiculous -- Moorgate & Liverpool Street & (& Liverpool Street), Barbican & Farringdon (& Farringdon), Bow Road & Bow Church (I think these are the same station, it's not entirely clear) and the two Shepherd's Bushes (on the same line!). Tavistock Street is going to be fun to build, if they're planning on running the Cross River Transit at the same depth as the other services in that area....
I hadn't noticed the two Shepherd's Bushes -- I assume that they'll rename one of them!
Bow Road and Bow Church are already currently indicated like that; there's actually a 300-or-so-yard walk between the two, and I wouldn't recommend it as an interchange in practice if you have any other sane option; particularly since Dwell Times at both stations tend to be O(5-10 mins) as well.