Firefly luciferase is widely considered to be superior to the Gaussia system.
Firefly luciferase is a higher order reaction that requires a second substrate. The absence of background autoluminescence in this system reduces critical signal to noise ratios in vitro and in vivo. Firefly luciferase is used as more than just a gene reporter. It is also used for in vitro and in vivo detection of proteins, small molecules and a few functional processes such as protein interactions and signaling. The color-shifting ability of Firefly allows dual/multi parameter detection/ imaging.
Because of the presence of background autoluminescence in Gaussia Luciferase, there is a higher signal to noise ratio, which reduces its efficiency. The Gaussia system emits blue light, which is good for in vitro luminmoteres but highly disadvantageous for in vivo imaging.