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I liked the spiral bike bridge thing that popped up a while back, is it dead?
Do you mean the Rotherhithe-to-Isle-of-Dogs bridge that was part of Sustrans' GOAL2012 proposals?
They still seem to be pursuing it, the latest I can see is here:
http://www.sustrans.org.uk/news/talks-underway-new-thames-cycle-bridge
It should have been funded by the Olympics and would be a good project. Not very close to the alignment of your commute, of course.
They did a good feasibility study back then.
Edit: Either they or someone else has put up a web-site:
You've picked a pretty impermeable stretch of London to traverse. :)
I'd probably go from Hackney Wick to Fish Island, cross the A12 at Old Ford Road (cycling and walking bridge), do Parnell Road, Fairfield Road (both fairly busy), then Campbell Road, Violet Road (various dog-legs), Morris Road, Chrisp Street, cross the A13 into Newby Place, and go east along Poplar High Street.
Unfortunately, if you get to the island on that side, there's no way of avoiding the big roundabout (Aspen Way/Cotton Street/Trafalgar Road/Preston's Road) unless you want to do the Blackwall Tunnel. It has been done, but for a regular commute you might well be ever so slightly too predictable. :)
Anyway, then Preston's Road, Manchester Road, East Ferry Road from the small roundabout (filtered in the middle), through the tunnel, etc.
It's worth trying, although in Tower Hamlets most of these fairly minor streets tend to carry high-ish volumes of through motor traffic because there's basically no attention been paid to strategic traffic management. And unless you want to go out of your way, the big roundabout is a given, unfortunately.
There have to be more (non-motorway) river crossings in that stretch--obviously, TfL's hideous Silvertown Tunnel proposal is not the answer.