I've only been lvl 40 a few weeks, and I'm already noticing a distinct lack of things to do.
But one major thing I notice is that there is no reason (benefit) to doing the missions I still haven't completed.
I've got dozens of them left, but all they give is xp (useless), resources (no big deal), or equipment (outdated).

If the rewards were changed to, say, resources and a 'merit note', lvl 40's could use them as currency to get other stuff that is needed. Whether that is nemesis/ unity badges, crafting mats, extra resources, etc.
It would mean I'd have a much better motivation for doing those quests, and explore all the areas I haven't been yet.
Sure, you could only do them once, so it's a temporary content fill, but right now I'm just not doing them at all.

I agree.
is it possible to have token for doing this quest again and maybe costume rewards?