(Reposting since my first post had to wait for mod approval and it got buried in the previous page): Have you considered unlocking the ability to buy some ammo types before you unlock the ability to buy the weapons they're for? I know that opening ammo boxes partially fills this role, but I find it plausible that say you could get approval for buying 5.56mm NATO after researching a looted M16 even if you don't have the contacts to buy more M16s yet; it'd add extra value to these looted weapons because they become usable in missions but cannot be easily replaced yet if you lose them.
Also, take this with a grain of salt, but coming from someone who played XCOM Files for the first time without having looked at any playthrough: Maybe you should specify somewhere in the starting UFOpedia reports that your first goal as a mission is to prove your worth to the UN by presenting an anomalous creature's autopsy to them (which I do admit makes a lot of sence insofar as you proving XCOM is needed), since that (and something else I forget) is what unlocks the First Report or whatever research topic, and there are plenty of research topics to prioritize over any autopsy if you don't know that.
In any case, sick mod yo. Having never played UFO Defense before (but lots of Long War and some X-Division, its Xenonauts equivalent), I first tried vanilla and Area 51, but found the game very overwhelming on soldier and inventory management from the get-go. I'm glad to tell you that XCOM Files is much, MUCH more easily approachable to a first-time UFO Defense/OpenXcom player due to the reduced stress that is starting with only two soldiers per mission and much less viable equipment. Thanks for all your work over the years, it has truly made the universe a better place.