Using a supercapacitor as an energy source

It'd have to be a pretty large super cap...

Honestly I think this is such an unique thing that I'm not sure. I mean, I guess but I'm not a super capacitor expert.

Do let us know if it does.

I plan on using a supercap for a project as well!  they are more expensive but have >1M charge cycles and can be quick-charged unlike a batteries!  Just be sure you control the max voltage per cell or it will be destroyed!  There are calculators for what the equivalent cap to a battery is.  The biggest practice difference is that a cap has a different discharge cycle.  It can by powered all the way to 0 v without damage.  Without a boost circuit however, as teh voltage decays, your top end speed also decays.  

I wonder what the application is? Supercaps will provide like a few minutes of runtime at best, and yes, you will need tons of them to get it it to a reasonable voltage.

This is not to say it will not work. A controller doesn't care where it's getting electrons from. there will be a quick voltage drop obviously but it will run until it hits the cutoff limit you set on the controller.