First off, I want to thank the devs for creating the Foundry tool! Terrific idea!
One, simple fix that's so very desperately needed (I know it's been mentioned before), is the ability to make NPC contacts invulnerable to collateral weapon / ability fire. In my own mission (and in many others I've played), the NPC contacts are killed during a fire fight with enemy mobs around them.
If the story requires you to speak with those contacts after killing the mobs, then the mission can no longer be progressed and the player must cancel out of the mission to reset the map. Very, very frustrating.
This one, simple (I'm hoping) fix would improve game play for many missions. Please implement this as soon as possible. Moving the NPC contacts far enough away from the mobs isn't always possible, and is often detrimental to the mission story line.
If we were to talk about a second most important fix: NPCs need to be able to treat walls, invisible walls, forcefields and objects as impenetrable assets... not things they can jump through, shoot through, and get stuck in.
I've been forced to drop many a Foundry mission for this same reason. The first rule of NPC contacts is to place them well clear of any potential firefight. This is essential when you're placing enemy mobs on a map and planning for combat. If one of your mission contacts is within running distance of an enemy mob, then you need to reconsider the design of your map.