Yeah, a soft reboot of sorts would probably be good, strip things down a bit and keep it simple. I think having too many extra NPC's was making it a little difficult to keep track of everything. 
Maybe changing the idea and having it be just our two characters and maybe one or two support personnel with us acting as a kind of 'silver bullet' type unit, going in and kicking doors down to take out high-value targets, be they individuals, WMDs, super-prototypes or whatever else, and perhaps still on the trail of Silent Line, just because a) it's a cool name, and b) it adds a narrative weaving things together nicely. 
It could also give us a reason to rejigger our GEARs slightly and make them a bit more exceptional if so desired. 
Just spitballing some ideas really to pump things up and make it a bit of a more robust idea for it being primarily just the two characters, maybe with just a couple of supporting characters controlled by each of us, rather than whole squads to deal with. Let me know what you think.