1. NPC Ranged toggle. This is a really persistent annoyance. You sometimes want to give certain fellow survivors a gun, especially on weapons missions. But you don't want them using them all the time, even at close ranges; they waste ammo and attract zombies, when a simple club or even unarmed attack will deal with your routine shamblers. Currently the only way to avoid this is to wait to give them a gun when you're almost ready to go at the mission site, which is a big old pain. It'd be nice to have a simple toggle to use ranged or melee attacks.
2. Weapon Selection: Having to flick through multiple weapons with tab when a zombie is in in your face is pretty unfortunate, especially when the ranged ones don't provide a melee defense bonus. This is really a problem when you're returning from a weapons run with five or six extra (unloaded) guns. Being able to go directly to the attack you want would really be good.
3. Being able to set your spawn point when going to the Fort screen would be rather good; having to run across half the fort, potentially dodging zombies when the battle starts is problematic (what, are you too stupid to sleep in the safe area with the rest of them?

4. Given the limits of the path and maneuvering commands, a function that would just randomize your survivors locations would sometimes get them out of no-escape positions that they've gotten themselves into (trapped behind a body pile, say, because the idiots followed you in there after you turned off Defend, even though you were no longer anywhere near that spot). This would avoid having to replay missions not because of any mistake, but fundamentally because of the limits of the software.
Just a few suggestions (perhaps not possible or too late to do any good).