The Spallation Neutron Source (SNS) facility at the Oak Ridge National Laboratory is designed with an upgrade option for a future low repetition rate, long wavelength second target station. This second target station is intended to complement the scientific capabilities of the 1.4 MW, 60 Hz high power first target station. Two upgrade possibilities have been considered, the short and the long pulse options. In the short pulse mode, proton extraction occurs after the pulse compression in the accumulator ring. The proton pulse structure is thus the same as that for the first target station with a pulse width of ~0.7 μs. In the long pulse mode, protons are extracted as they are produced by the linac, with no compression in the accumulator ring. The time width of the uncompressed proton pulse is ~1 ms. This difference in proton pulse structure means that neutron pulses will also be different. Neutron scattering instruments thus have to be designed and optimized very differently for these two source options which will directly impact the overall scientific capabilities of the SNS facility. In order to assess the merits of the short and long pulse target stations, we investigated a representative suit of neutron scattering instruments and evaluated their performance under each option. Our results indicate that the short pulse option will offer significantly better performance for the instruments and is the preferred choice for the SNS facility.