Navigating Bow roundabout/flyover

I'm not familiar with Bow roundabout but I'm assuming that cyclists don't use the A12 and therefore practically all bike traffic goes straight across it east-west and vice versa.

Wouldn't an obvious but expensive solution be an extra pair of flyovers that take cyclists (and pedestrians) straight over the top of it?

Well, there's obviously not a lot of cycle traffic along the A12. You're also not permitted to cycle along the A12's M11 Link Road bit (the legal situation in the bit between the Blackwall Tunnel and Bow at least, possibly up to the A12 Lea Interchange, seems to be that you can, although few would choose to--I've been along that bit, but not recently).

When you design junctions, the two things you want to avoid are increased junction envelopes (always create poor crossability, a lot of severance, and reduce room for joining up the 'grain' of the city, e.g. development on the corners) and grade separation (flyovers, underpasses, etc.). You can't even offset the disadvantages of large junction envelopes by grade separation. Avoid over-complication and make sure that London maximises its historical advantages--that unlike most other major cities, very few urban motorways were actually built and that we now have a chance of seeing these mistakes for what they were and cut them back. This includes small junctions that make people actually stop and interact and trade there, creating human-scale environments in which there is less need for endless travel and estrangement.

Motorway - The Kinks 1972 - YouTube