It's not the technology. A lithium battery discharged that much is putting a lot of drain on the charger, and a charger that can't take it isn't putting out 5 Volts any more (that's just how electricity works). The stock charger is probably built to handle more current drain. (My phone can't draw more than 1200 mA, but the stock charger can put out 2000 mA - some of my chargers can't put out more than 700 mA.)