Glad you enjoyed it overall! To address some of your issues:
- I've already planned a v2 of the familiarity system, which should smooth over most of the biggest problems with the current one (like the rover actions being different bonuses between locations) - Familiarity v2 on the Roadmap.
- I do plan to add a toggle option for saving the resource priorities between loops. Personally, since the preferred priorities wherever you end a loop are unlikely to match the ones at the start of a loop, I'd rather they reset to auto so I don't forget to change them and the character does something stupid. But I can see why people would want the option.
- Combined actions are also queued for an upgrade. The main thing will probably be making travel actions appear both inside and outside combined actions, so that you can still travel.