It would be nice if you could just dump all of your mods, armor, and weapons collected while adventuring in a central location ( your ship). When you want to modify, equip, or break down gear, it can pull from your ship's stash, while you use the ship's workbench. This is the same functionality seen in Diablo 3, for example. I think Fallout 4 may have had it as well.
Additionally, it would be nice to have a quick - "deposit all items" button. Also a "tinker to max" option.
The stash having additional filters for quality would be nice as well.
Right now the mod stuff is neat - but inventory management is kind of tedious.