It seems to me it may help to break down the task into two smaller pieces. (At least 4 my simple mind it will). :?
1. A switch network that will rearrange the grouping of individual two terminal bi-polar devices from a serial chain to a set of shunts.
B. Implement a capacitor bank to serve as a turbo boost pack.

Switch Network
If you really prefer a hardwire solution, then it doesn't matter if you're talking about caps, batteries, leds or whatever. Figure out a mechanical switch arrangement using batteries first. The electrical characteristics of supercaps actually function more like batteries rather than conventional capacitors anyway.
Essentially this identical requirement was posed a while ago on PA by someone who wanted a simple way of switching 3 SLA from their 36V series connection when in use discharging, to 12V in parallel for the purpose of charging. Reason being (obviously) he only had a single 12V charger & was tired of constantly pulling wires on & off as well as save wear & tear on the wiring. I believe the concensus of the brain trust was that it's simpler & cheaper to buy a couple more chargers. But if you figure it out, I'm sure there are numerous tightwads that will be grateful.

Supercap Turbo Pack
Supercaps have been demonstrated on several prototype electric cars, so the idea seems to have merit. However for motive applications I have basically written it off as pie-in-the-sky for my purposes. Primarily due to the price & that I can't get ahold of the very large sizes in small quantity. By way of example, the largest size I can readily lay my mitts on is from DigiKey. Which ones did you have in mind?
50F aerogel, 2.5V, 25 mohm ESR. Dia. 18.5mm, length 42mm (4/5A size)
Unit cost $23.80, $1660.00 hundred lot.
http://www.digikey.com/scripts/DkSe...earch?vendor=283&mpart=B1840-2R5506-R&site=US
Additionally they fry rather quickly with slight overvoltage & do not have a flat discharge curve, but those problems can be dealt with the proper circuitry. So I would have to be strongly convinced, why bother with caps, what's the benefit? I would agree that the A123 gives you
way more bang for the buck & has cut them out of contention. At least until their price comes down, which I would expect at some point because there's really not much to them.