I have collected several chests/containers that are in my box in camp. I have sorted my inventory into these containers, one with books for example. It's relatively easy for me to add any books I find to it, so that part isn't really an issue if you think for a second about it.

As for the quest log showing you were to go, yes it totally does if you know where to go. There's a "show on map" button at the bottom of the log.

To pause, enter turn based mode. Shift-space on KB&M, or the button on the button right next to the camp button, where end turn is in combat. I somewhat agree in single-player, esc should just pause as well, but it really isn't an issue worth worrying about.

The rest of what you said, yeah I agree with. Probably the most frustrating thing you've mentioned is the fast travel not allowing you to see other maps. I remember where each one is, but it'd be easier to select it on a map for some of them. They're ordered based on the order you found them, so close ones may not be grouped.