I don't know if this is doable, or already in the game and I haven't seen it, but here goes.
I'd like to be able to obsolete and/or auto-sell equipment. This could perhaps be done through the vault screen, filtered by all bases or on a base by base setting.
After a while, getting rid of certain types of equipment is an automatic action at the end of a mission.
There are a couple of potential issues here, such as items being prerequisites for research and manufacture. This needs to be considered, but I think a feature of this type could help with tidying our vaults.
There is already a system for creating item loadouts and saving them, so perhaps a variant on that system could be used?