I think the first thing to bear in mind is that the game has been under active development for twenty-two years, with an active community giving feedback and suggestions for almost all that time. Many, many people have bounced off the UI or the mechanics and made suggestions to improve them, although usually in a more constructive way.
Secondly, its a part-time hobby and a freeware game, so development priority is given to the most interesting elements of the game. UI is a long way down that list 
so any necessary UI elements usually get tagged on at the end anywhere they will fit. Over time, the UI starts to resemble sedimentary rock as more layers are added. Occasionally, I go through a window where the UI has got particularly obtuse and try to improve it - you are seeing the improved versions in most cases
Orders are complex. There are currently 117 different orders and each one has movement requirements and restrictions and some have destination requirements. Working out every potential combination of effects in any situation is complex and would be even more so if orders could be re-arranged at will, or random orders tagged on the end. So there is a strict precedence to orders issued and any conditional orders triggered will replace the current list.
The alternative is for me to spend endless hours calculating and debugging all those potential situations. That is never going to happen because I’ll never generate the level of enthusiasm and perseverance required and I would rather spend my available free time adding new features.
Shore leave is required for game balance and to add an extra layer of decision-making to ship design and deployment considerations. When the ship is actively carrying out orders, the crew is not on shore leave.
Toggling events is in v3.0: Aurora v3.0.0 Patch Notes - Unreleased
The tanker flag covers more than just movement orders. Also, there are too many potential movement orders to show them all, especially as many would be irrelevant and and even the relevant ones result in a long list. Instead of adding logic to deal with the player issuing irrelevant orders, I exclude them in the first place.
The various questions about stabilisation, purchasing minerals, fuel production, etc. are really “Why is there no tutorial or manual”. The game is very complex and has hundreds of buttons and other controls, so that a manual would obviously help, but again it comes down to enthusiasm and priorities. This is a hobby so having fun is the priority rather than being focused on increasing accessibility or maximizing the number of players. However, the community has created many excellent tutorials and let’s plays and is very responsive to question on here and on the Discord.
However, having said that, if you have specific constructive suggestions about how to improve the game, along with the rationale as to why it would improve gameplay or QoL, then please put them in the suggestions forum. I’ve added hundreds, probably thousands, of players suggestions into the game over the last couple of decades.