Is it just me, or is charging via usb not as good as using an outlet?
When charging over a USB port which is also used for communication, you're limited to 2.5W/500mA.   When using a port dedicated for charging (which can be a female USB-A plug), you can use almost 10W/2A.  From these numbers, the dedicated charger is clearly better.

However, batteries have thermal and chemical properties which often limit the charge rate to something less than these values.  This is especially true for small batteries in confined spaces like your cell phone battery, and the lithium-ion chemistry which is likely used has the added potential of explosive thermal failure, so the charge rate is limited by some circuitry.  

It would be reasonable to assume that the maximum charge rate for your cell phone battery is a little less than 2A and more than 500mA.  Cell phone batteries are usually charged at about 1C, and the maximum cell voltage of a Li-ion is about 4.2V, so assuming a 1000mAh battery and a 90% efficient charger (which is generous), you'd need 4.6W of power to charge your battery as fast as possible. 

Charging more slowly than this (i.e. at 2.5W) shouldn't diminish the charge level of the battery in any noticeable way.  A software power meter could be erroneously reporting a higher battery life due to heating of the battery and the consequent higher voltage, or any number of other errors.  If an accurate test (identical use patterns, signal strength, previous charge levels, etc) indicates that your phone has markedly less battery life after charging by USB, then either your battery is defective or your phone circuitry is poorly designed.