I don't neccessarily think that the Massassi are easy prey for Storm troopers, and if the Massassi hole up in smaller chambers and rooms they remove the number and distance advantage of the storm troopers. Likewise, Sadow can probably do at least some illusions admidst the chaos, which would take Sidious' concentration to attempt to identify and dispel.
If we disregard the force powers of Sadow and Sidious as an influence on the war, then in a long distance battle I'd say the storm troopers curbstomp the Masassi.. However the Massassi are superior to the storm troopers in hand to hand combat.
Janus, are these the elite troopers that are empowered by the dark side?