Initially my circuit had only a 10uF capacitor after the diode bridge, this turned out not to work and confuse the phone a lot. After increasing this to 230uF by adding a 220uF capacitor everything worked well, but a 470uF probably works even better.
Here you can see the circuit actually attached to the bike (using electrical tape for insulation). You can see the Nexus wheel at the bottom and the USB connector with the plug heading to the phone. As you can see there is one wire hanging loose, this is the ground wire, which is not needed as the alternator itself is already grounded to the bicycle. I prefer to leave it disconnected to avoid ground loops, although it is unlikely this will happen.
There is also a switch, shown here from the side, which allows you to turn off the circuit (which will make it easier to cycle, as there is hardly any resistance from the in-hub alternator if there is no draw) or switch the power directly to the front light of the bicycle, which was the original configuration.
The final question is whether it works, and it does. The first trip I got 2% charge (from 28% to 30%) the second trip 5% (from 90% to 95%) and the third trip 8% (from 66% to 74%). This is while the phone is operational (and actually syncing Email in the Mountain View WiFi area).