Some general thoughts about supercaps:
How much regen current can your controller generate?
How much regen current can your battery accept?
How much charge current can the supercaps take *at the voltage they will already be charged to* for the battery level you'll be at?
Remember that the energy the caps can hold is finite, just like a battery, but unlike a battery that energy is spread thru the entire voltage range from zero to the max they're rated for.
A battery has that energy all concentrated in a very narrow range around it's nominal voltage, which is what your system is based around and operates from.
So almost all of the energy the caps can accept or provide is outside the range your system is capable of using, unless you use external electronics (which waste power in both directions of the conversion) to convert the supercap energy into the voltage range your system can use. That conversion system is essentially what the paper discusses.
But it's almost certainly cheaper, smaller, lighter, and more efficient with less potential points of failure to add more battery cells or use better ones that can directly handle the regen currents and the discharge currents, than to use supercaps.
Supercaps are one of those things that people keep coming back to, trying to find a way to use them instead of either the existing better-working, simpler, cheaper solutions, or making a new technology that could replace them both, or improving one of the existing technologies to not need these bandaids.
Supercaps do have their uses, but they also have some pretty severe limitations.