2. I think that when assigning items to the hot bar, they should stay assigned until manually removed...
This. I felt the pain again and again in D:OS EE xD
The suggestion of FrauBlake is good tho.
1. At the moment we are unable to access the contents of rucksacks during a trade...
I only took items in sacks I didn't want to sell so I wasn't even aware this. But if it is like that, then the perfect solution would be the same as was with the crafting window in EE, when you open a sack while trading then it replaces your inventory window to the contect of its own - having a 'Close' button to be able to go back to the original view.
3. And finally, I'm sure others have mentioned this, but tracking quests...
This is the subject of the most arguments on forums

The majority of people (including me) is against it. Yeah sometimes it can be pain in the arse, but at the end of the day, it feels good to find things out on your own. This is my opinion at least.