Take two one Farad capacitors and charge them to 1V. Energy stored in each is 0.5 Joules.
As capacitance is defined as the ratio of charge over voltage, the charge in each capacitor is one Coulomb.
Connect them in in series, and you have two Volts across them. Discharge them through an integrating current meter, and one Coulomb charge is measured, as the same current path flows through both. The total capacitance of the combination is 1 Coulomb/2 Volts = 0.5 Farad. The total energy is one Joule, either because you have two capacitors at 0.5J or from the formula ½C∙V².
Connect them in parallel, you have one Volt across them. Discharge them, and you measure two Coulombs as the current from each are added together. So the total capacitance of the combination is 2 Coulomb/1 Volts = 2 Farad. The total energy is one Joule, either because you have two capacitors at 0.5J or from the formula ½C∙V².
But in both, you can swap the capacitors over from one topology to the other at a given state of charge and the capacitors themselves don't change.
If both capacitors are fully charged, so the energy stored is at the maximum, and switching topology would mean "a huge amount more storage available", then you could charge them in one topology then use a relay to switch them to the other, and use this extra energy to charge another bank, and so create a perpetual motion machine. In reality, the amount of energy storage capacity is the same.