As I've said before, I do keep useful things at the top, but I'm always switching out hold items, so they get stuck at the bottom anyways. That's the part that bugs me.
In the old games, I never had a problem with running out of room as I always put anything I found and didn't need right away in the PC. The bag being bottomless is nice, though, and I wouldn't change that, but it'd be nice to have the PC too since I don't need all my items all the time.