Re: why it takes upto 3 minutes per % to fully charge samsung note 3 neo(3100 mah).
There are a myriad of possible reasons why that would happen... The usual culprits (and the easiest to troubleshoot) are the cable and/or charger. Try switching USB cables or using a different USB charger to see if it improves. Remember, the less mA your charger can output, the slower the charging will be (old chargers and many PC USB ports can only output 500mA, whereas modern chargers range from 1.5 to 2 Amperes).
If that doesn't help, then things get trickier. It could be a battery that's dying or defective, or a bad charging port/circuit. It could be the software (unlikely) but you can try charging with the device off and see if the time improves.