Are power systems that rely on batteries limited to 25% efficiency?
Not at all, for batteries that approximate capacitor behaviour (Which is to say nearly none of them) you charge with a current source not a voltage source, which is potentially very efficient. 

Batteries that behave as a voltage source in series with a resistor (Where the resistor value appears to vary) you charge with a current limited constant voltage.

Now on discharge, maximum power transfer occurs when RSource = RLoad, but we don't want maximum power! We want (somewhat close to) maximum energy, so we make sure the batteries internal resistance is much smaller then the apparent resistance of the load.