This isn’t exactly a priority, and only really affects those that run more than one system, but…
Something I would love is the ability to have separate “profiles” for different worlds we have. That way when managing mods, we would only see the mods that pertain to that specific world. I’ll give an example.
Example:
I run a weekly Starfinder campaign. It has mods for Starfinder installed. I’m getting ready to start running a weekly 5e game, as well. I would love a way to setup each “world” to only see the mods I intend for them to see. So, one profile we’ll call “Sci-fi SF” will see all mods selected on that profile and only be seen on the Starfinder world that I set as that profile. Then another profile “Fantasy 5e” would have mods I want seen by my 5e world. I feel like it wouldn’t be terribly hard to implement, basically each profile would create a list the world would then read and apply as a sort of filter to what mods are installed. The big question is if this would be popular and helpful to others, because it would certainly save my sanity!