My wishlist:
Add 30-50 notables to the atlas tree so there's a feeling of actual choice and more of a progression curve when doing maps.
Fill the maps with actual content or make them smaller to fit the level of content within them. I do not want to slowly walk through a huge, empty map with a cancer layout.
Rework the watchtower system to not be so tedious. Scarabs are great, might as well go with those since we know they work.