Galaxy S5 charging slowly despite 'AC' and 2A charger
Your understanding and measurements are logical and I can't say why your battery should charge slower compared to the earlier one 

One thing you may try is to backup your device and flash latest stock ROM or custom ROM which has a kernel that permits higher rate of charging

If that's a lot of work, change the USB cable to a thicker one. See my answer here for details

(I am not affiliated with the product but a happy user. I keep buying those when on discount and gift to friends. All have uniformly attested to better charging rate)

Edit : It could be a faulty USB port too. You could try getting that replaced