Massive ultracapacitor banks, why don't they work? (400V 3.38F)
There are a couple of reasons.

First is energy, E = 0.5*C*V^2 so capacitance is not as important as voltage in this regard. 

Coil guns need an incredibly quick pulse of current to work effectively. Think of this in terms of a time constant, RC. If you have a larger capacitance, the bank will discharge slower and the field will be present longer which (if the projectile passes the coil) will actually slow it down.

Also, think of the ESR of a capacitor. If you have hundreds of caps in series, that ESR will be through the roof compared to a bunch in parallel. This will also increase your time constant.

Super caps are nice, don't get me wrong, they just have their own niche uses.