Automatic switch between parallel and series connections
Use electromenchanical relays with changeover contacts. They have life operations in the tens of millions of cycles and if you needed to switch one every ten seconds, then you get over 1000 days before you might need to service a breakage. Toggle the relays with a low frequency oscillator but you are then wasting energy in the relays (as you are when using human intervention to manually operate switches).

Or use SSRs (solid state relays). A bit better efficiency compared to normal electromechanical relays of course.

However, I note what you say about the minimum voltage being 0.2 volts and I would like to point out that there are offerings from both TI and Linear Technology that work down at this level to produce 5 volts on a super cap. You also mention efficiency and I think you are somewhat misled in thinking that dumping charge from one capacitor to another is an efficient process - it isn't because the energy lost is 50% for each cycle. And you are doing this twice per cycle - once when you parallel the capacitors across the primary energy source and then again when you try and raise the voltage across supercap 3.

I think you need to look at the losses and ask yourself big questions.