Charging ultracapacitors separately and using them in series for regen braking system
While what you propose can be done in theory, it seems impractical compared to alternatives.  The various switches, and controlling them, to combine the capacitors in different combinations won't be easy.

You said yourself a DC to DC converter is another option, but ignored it.  That seems like a simpler system, and most likely you will want such a converter there anyway for other purposes, like charging the battery from long downhill slopes.

This also begs the question why you are using capacitors in the first place.  Why not have the motor charge the battery during braking or long downhills?  The energy density of capacitors is less than that of batteries.  Since the batteries have to be able to produce the maximum current into the motor, they should also be able to handle about the same current in reverse charging them.  What do you think the advantage of a mixed capacitor/battery system is as apposed to just a battery?  I suppose they are more efficient short term storage, but at the cost of considerable bulk and weight.  Of course that weight decreases overall efficiency and the extra space either makes the vehicle less usable or presents more wind drag at high speeds.

I haven't done the calculations, but I'm skeptical that adding enough capacitance to store the kinetic energy of the vehicle makes sense.