Hi,
I remember that Fairphone had to correct Android 5 to allow the FP2 to recharge from small current of normal USB port.
This seems gone with Fairphone OS 17.06.4 (Android 6).
I 1st thought it was the battery draining (in my case caused by adaptative screen backlight) which was overcoming the 500ma for USB current. But it’s not the case, with no more battery draining it’s still unable to fill up the battery.
From “How can I charge my Fairphone 2?”:
A charger for the Fairphone 2 needs to have the following specifications:
5 volts (5V) 1 ampere (1A, 1000mA) or more micro USB Type B connector
Common USB ports (~ 500 mA, supplied either from a PC or a notebook) are not recommended.
My point is that it used to work and I lost these feature upgrading to Android 6 (with no warning).
Regarding batteries, what is recommended is : the slower you charge, the least you worn your battery. So I recommend to recharge from standard USB ports.
Then, there are a lot more standard USB ports available in your everyday life than special charger device.
In fact the EU decided that every phone have to be able to reload from standard USB ports, and with good reasons 
Maybe the developers found an issue with a setup that is similar to yours and decided to withdraw support for it.
That is true if electronics were not designed to better regulate the charging process. The phone as well as the battery come from the same manufacturer (Fairphone), so someone can expect both do match pretty well to each other.
This is not true. I used to charge and I’m still charging my phone on the USB port of various computers and on the USB port of our router. The only difference to Android 5.1 is that now in Android 6 on the locking screen it reports that it is charging slowly when connected to a USB port instead of a dedicated USB charger. So your issue seems to be somewhere else (bottom module?).
Just like you I expect that a slower charging process can extend the lifetime of the battery. Even though phone and battery come from the same manufacturer charging slowly puts less stress on the battery due to lower current flowing and a there are a few more influences. Fairphone just like any other manufacturer cannot trick physics and chemistry.
“In fact” means you have a source for that?
In my recollection the EU only decided that charging had to be done with the same method with all smartphones, and the smartphone vendors chose to comply by introducing Micro USB. Wikipedia seems to stop at 2014 for that matter, so perhaps I missed something.
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