What exactly do you want this project to be? FS-like space-sim? What engine and technology do you want to use here? Current description is not explaining much about technical aspect of the project. As I know from my own experience, idea is first and the easiest step.
I am currently planning to work with FS_Open, but I am not averse to switching to Unity if technical problems become unurmountable - and right now the only big ticket technical problem I see is beating the Campaign Editor into submission.
As for genre, thanks to work Spoon and Axem have done for Wings of Dawn, I was able to scale the narrative ideas into a FS-like frame (exploratory looks at the VN-script and weapons crafting suggest that it could be retooled for my purposes) - originally I was thinking of going more into a cap-ship command angle, but since the model of warfare in Pendragon is heavily reliant on UAVs anyway it was an easy fix to go there. Basically instead being a fighter pilot, you use telepresence from your control ship to fly your "fighter" (and just to keep the stakes, there are penalities for loosing a drone other than drone being unavalible).
Speaking of Control Ship, the idea is also to add a layer of ressource and crew management to the mission-per-mission proceedings, think of a mix of Persona 5 and Battletech - i.e. each "step" in the campaign is on a timer, waiting has its advantages (esspecially to recover from penatlies) but acting faster will yield higher rewards. (part of the mechanics nearly made it into Vega must burn - but that campaign is too short to do repair times on your fighter supply)
To illustrate:
On the structure: The first three Episodes, subdivided into chapters, are about getting the cast assembled and universe presented - the fourth Episode is then supposed to be an three (possibly four) faction race for an objective outside the territories of the human factions. There is no fixed number of missions per chapter, but they are supposed to have at least one mandatory mission.
Episode 1, Chapter 3 starts with the Pendragon (let's call her that for now, placeholder is Esarai's Emperor (https://wiki.hard-light.net/index.php/Emperor)) having just made a narrow escape from an enemy force. Between events of previous two chapters the Pendragon is supposed to be in bad shape, most systems are down and she had left port without a full crew compliment anyway, so the losses among the crew count twice.
However thanks to the cricumstances of their escape, the Pendragon is safe for now - even to the crew it was a miracle that it worked. But now thoughts turn towards recovery, as well as planning to "fix the situation". Plans are made to bring the Pendragon to an out-of-way base where the Royal Guard keeps some of their Commonwealth-era tech, including ships they don't have the manpower to crew. But considering the movements of the enemies involved, the anchorage may not be safe to visist.
Going right away will mean that you have to defend a severely damaged Pendragon, so the mission can fail more quickly. Waiting some "turns" will off-set the damage to the Pendragon but it will also mean that between the arrival of the Pendragon and the arrival of the enemy force less supplies will be loaded, meaning at very least you don't get upgrade points (read: repairs) for the Pendragon's systems. If you wait too long, you might also have additional penality of the new drone operator not being avalible right away. (This is the stage at which Crew Penatlities would get introduced.)
Anyway, if you complete the mission you gain a "scout ship" (placeholder Esarai's Phoenix Rising (https://wiki.hard-light.net/index.php/Phoenix_Rising)) which is basically the tool through which you then have the option to do optional missions for additional rewards, but now the enemy as a lead to hunt for the Pendragon, so you are back on a timer.