Hi Nicholas, I might not have the solution, but I have few suggestions/ideas. Hope it makes sense and that it will help you somehow 
to : Why doesn’t Asana allow us to see all subtasks in the list view? It’s not a very effective way to add a lot of subtasks to a project.
→ The reason is because your subtasks are linked to the parent task and not a project. If you only need to see the subtask you can try using advanced search. I think this is the only way to do it without any modification of some sort. You can save the URL if you always need the same one.
→ If you need to be aware of progression perhaps you can try creating a new board where you add every subtasks only. So you can define column or tags to give you information or trigger some specefic automation without breaking the principal board you already have.
To : Is there a way to represent the structure of my project, such as system and subsystem names, and create tasks that are referenced to this lower level of subsystem?
→ I believe that, if I got it right, what you are looking for could be done with an action drop down : 🎥 An action drop-down in Asana: a game changer for automation
To : Is there any way to create all subtasks with parent assignment and project association?
You might want to take a look at what you can do with imports. Yes you will have an other tool to use, but I really think you could save a lot of time if you have to create many subtasks/tasks at once or if you have many tags needed. It will only works for new tasks/subtasks, but the importation will link everything for you in that matter.