Capacitors and energy losses

A favourite A-level Physics problem is one where a capacitor C₁ charged to a potential V is connected to another uncharged capacitor C₂. It is found that the initial energy of the capacitors is greater than that of the combination. The loss in energy is ascribed to various agencies such as joule heating of the (excluded) connecting wires or radiation losses. Students find this an unsatisfactory argument and even express doubt as to whether C₁ and C₂ are actually in parallel after the connection is made. After all, if charge flows from one to the other, they are actually in series. If resistance is present, the capacitors are clearly in series. The author tries to find the correct version.