Put simply, make the ‘go here and kill stuff’ missions smarter. Just today I’ve had to backtrack three times in about 6 hours of gameplay to places I’ve already cleared out just to pop missions I picked up later that required me to go there and kill a bunch of enemies (which I had already killed before even picking up the mission).
Particularly good example of this is the one in Småbåtshamnen that you pick up at Hisingafyren. In-universe, I would have just written off the whole thing (been there, already saw what happened, might check back later on my way back up the coast after dealing with Torsberga). In terms of actual gameplay, it was a pain having to fast travel to the closest safehouse and then travel 2-3km over rough terrain just to have the mission complete the moment I set foot in what the game considers to be Småbåtshamnen (and get ambushed by not one but two FNIX harvesters on the way that dropped essentially nothing after me having to empty half my inventory killing them), then double back to Hisingafyren so I could clear out Lysehamn and Torsberga.
From a programming perspective, the missions should check when picked up if you’ve been where you need to go already, and if you have check if all the stuff that you should have killed is already dead. The second piece of information is obviously already saved (otherwise the mission wouldn’t auto-complete when you get there), and the first should be pretty easy to check in most cases.