By this do you mean building a back-to-back link between London Bridge and
Waterloo, making them both straight-through stations? I think that would
be a great idea, to give the trains a non-terminating run straight across
the south side of the city centre, and making the north-south journey to
reach this route from places in the city centre a much shorter one. It
involves no tunnelling, so should be cheap. Well, cheaper than Crossrail
and coping with existing traffic rather than creating new.

Michael Bell

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I'd have it run on the south of the station along Lower Marsh, across
Waterloo Road, to meet the existing line at around Hatfields. A
flyover could be put somewhere so that trains could turn into Cannon
Street.

On the subject of Cannon Street, I've often heard about the slope
being to much, and the vaults being in the way. However, it's just the
lines that need to be linked, not the stations. Its not a cheap option
and would cost a lot of money. But it could be more beneficial than
Crossrail.