It's becoming apparent that with the monumental tasks ahead of the party that the NPC's will have to be employed to take care of a lot of different things simply because the players don't have enough hands to do everything and also because in some cases the players don't have the necessary skills to tackle an obstacle where as an NPC might.
The key thing to keep in mind here is that it is the players that are important, not the NPC's. What this means in a broad stroke is that
when an NPC performs a task whether mundane or specialized they will not have the capacity to affect change quite the same way a player would with equal skill level,
meaning that what the players achieve will be all that much more highlighted by contrast. What this means to you, is that you should not expect a Duex es Machina/deliverance from the NPC's. I will always have a reason as to why they can't simply solve the puzzle, win the game, end the war, etc. for the players.
Again the story is dependent upon the actions of the players. I won't dumb NPC party members down because they are what they are (for example, Six is an expert assassin and is likely considered superior to the party members in physical combat in most scenarios and that would be reflected, but he wouldn't unlock anything that a PC might other than possibly a plot hook), but I'm not going to give them any special moments of brilliance on behalf of the party unless they flat out crit on a roll (1,1,1).