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Not sure what you're getting at...?
It currently has two female USB-A ports. I'd worry that replacing those with female micro-USB ports would end badly as they aren't too strong. Also, cables with micro-USB at both end aren't very common, so you've got the same problem as a weatherproof connector!
Does anyone know if you need other conductors beyond the +5V and GND to charge? (ie is there feedback coming from the device being charged?)
Thanks for the reply. Your comments re a cache of sorts make sense, it's just a bit of a faff (but a faff common to all devices of this kind I guess).
Re the ports, you're right - but having the ports externally would allow you to reduce the size of your housing (as well as reduce the risk of breaking ports in your monolithic device). Of course, it would bring other problems in instead - now you have a different port to keep dry, and non-standard cables. At least you can use a type of port that's designed to be weatherproof.