There will be launch bays as modules / sub-systems, the first tier will be for drones. These will operate under a simple 'orders' system where you will select, say 'guard me' etc. later on in the game there will be Fighter Bays, which will house fighter craft, and will require pilots on your crew to pilot them, these will also have a similar orders system.
The way you laid out your game-progression is essentially what we are going for. We are using a very agile design philosophy where in nothing is set in stone, and we will and have changed things because a new idea was better.
as for managing fleets, we would like to really, but it will not happen in our initial release, we are only 3 people and I will not allow us to promise something we cannot deliver and over extend ourselves.
Other than that, all suggestions and ideas are extremely welcome! feel free to post on our official forums at www.KineticVoid.com