The main effect to the user is only that thin film panels are larger for the same power rating. Since you are buying Watts and not efficiency, there is little or no advantage to paying for the super-efficient panels unless you are very tight on space. Although thin film panels were supposed to end up being cheaper, that has not happened to any great degree. Thin film panels do not lose as much power at high temperatures - all panels lose power when hot, but the drop off is less. These differences are not great, but if other factors are equal it may be the deciding reason.
Efficiency is based on how much of the sunlight that hits the panel is converted into electricity.
The sunlight hitting the earth at sea level on a bright clear day is about 1000 watts per square meter. You have to watch how panels are rated. Batteries need AMPS, not volts to charge. Efficiency is only really important in that it determines how much space a given wattage panel will take up. Some panels, such as the Unisolar, have built in bypass diodes around each cell.