This, so much this. It annoys me to no end how the spawn positions of everything are randomized. Case on point: I wanted to add some fighters to the Longbow Sea Base map as set dressing, so I set their spawn area to front... but then instead of appearing in the airstrip area as I expected, they started to pop up literally all over the base, including inside the command bunker. Another time, I wanted to place an interactable computer in a certain room in a Fifth Column base, and were quite displeased that I had to look for it in several different places between test runs. Because of that and many other things, I second the wish for more control over spawn locations for NPCs and objects.
One other thing I'd personally appreciate is letting the players build their own mission maps. Not asking for anything to the extent of SG base building, but seeing as most instanced maps really are a mish-mash of preset rooms and hallways from a list, I believe allowing the players to take advantage of that would greatly increase mission variety. Even better if we could combine multiple different tilesets per map.