I am working on a battery powered data logging application. I will be using a lion battery as power source, which will be charged over the usb connector. Basically this is nothing special and this kind of setup has been discussed here in several posts. I just might have a suggestion for an improvement to your superb board: for application which require to be powered by an external source over vin, but also in case of a usb connection by vusb, you could move the solder jumper between the two anodes of the allready installed diode. Now several setup are possible:
1 - jumper closed (not cut through) is just the same as now
2 - with the jumper open the board can either be powered by usb or vin.
Now this is not so new, but has the benefit, you wouldn't have to add extra diodes externally which add extra voltage drop (which may make single lion cell applications harder ). The allready placed diode should be able to handle the power disipation on just one diode, probably you would have a slight increase in voltage drop, but this would be much lower than having 2 diodes in series. Basically it would be no change in the BOM, but only a layout job.
Another suggestion would be placing a voltage divider from vusb to an digital pi, so one could detect if usb is plugged in. In my use case, this would help me have the board run in low poer modes while gathering data away from the usb host, and switching to full performance when retrieving data with a usb connection.