This started cropping up a bit in 4U as well but I'm feeling it even more this time around: There are too damn many account items now. Even with the field pouch helping out I'm running into a lot of "item pouch full" management issues any time I want to do some actual gathering and I feel like a lot of what's being picked up is just kind of there to take up space.
Have you tried using the cat at base camp? He will send a whole inventory's worth of items back to your storage box for you once per quest. I don't think you can return account items but at least you can send back the other stuff.