Have you tried 'telling' the battery how much capacity it has again? (Drain until it automatically shuts down due to flat battery, charge back to 100% while off, switch on, drain again, charge again and use as normal)
Many manufacturers recommend charging when you reach 15-20% during normal use.
Also, have a look at govenors/schedulers if you have a custom ROM installed. Maybe changing combo works better for you, or even changing combo and switching back.
Sent from my Nexus 7 using xda app-developers app