I liked the depiction of the Military in the previous game, as well as the feeling of authoritarianism that they gave Boston and the other Quarantine Zones they controlled. The World War Z novel-style blue uniforms and riot gear were kinda cool as well.
I'm not sure if they'll be in Part II, though. That said, Denver is implied to be an operational Quarantine Zone, and I think it is located within a reasonable distance of Jackson County. I think the Fireflies are implied to be returning, and I suppose the Military is an important moral contrast to the Fireflies, as well as the reason for their existence.
Like the first game, if they are in Part II, I don't think they'll play an important role in the overall plot; they'd probably just be one-time enemies that are on patrol or something, who would only engage our heroes because they're in the wrong place at the wrong time. Still, I hope they make an appearance!
What do you guys think? Will they show up?