Hey! Welcome, well, let's see what we can do here...
There is a method (in the FAQ forum) to just setup one route and fly arbitrary flights against that
You can probably use the 'airlines' to be squadrons, since pilots are assigned to airlines
You can use routes with this, in conjunction with the arbitrary routes feature
Yep, it's possible to manually change and not do it by hours. It's a setting in the config file, then you can manually change them.
We have a few airlines who are using it in a military context, seems OK for them. I have made changes based on requests (like having the same arrival/departure airports allowed, a few other things too, so if you have pinpointed ideas, we can check them out and see what we can do. I would say most of the things happening now are by request...
Also, check through the core/app.config.php and core/local.config.php files for settings which are available. And check the documentation too