You missed the entire point. You cannot get better than 50% efficiency in charging a capacitor from a voltage source with a linear circuit. The actual reason is the mismatch between the source voltage and the capacitor voltage.This helps get a clearer picture of what we might have to upgrade to reach some target efficiency like 90 percent.
It is easily understood intuitively by realizing that the power drawn from the battery is the current times the battery voltage, whereas the power going into the capacitor is that same current times the capacitor voltage, which is always lower than the battery voltage. Mathematically, you must integrate both over time and you will see that the energy stored is 1/2 the energy out of the battery.
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