Ideally I'd love to see the game officially have a point based system where you can buy your starting ships, weapons, officers, skills and faction relations.
Perhaps, but if you gave the player X number of points and then allowed them to spend those to buy ships/weapons/officers/change relations/etc. then the system will undoubtedly end up being cheesed by people, say, putting all their points into a phase ship or something and either A) stomping the entire early-game or B) running out of supplies and raging at the game for being dumb.
It would have to be a carefully metered mechanic, and even then may end up causing more confusion (with yet another number the player has to keep track of) than is worth it. If I was to use such a format for Better Beginning, I'd present it as an initial number of credits that the player can spend to buy ships and additional weapons/goods (from a limited selection), similar to how you might choose to play in a normal game if you skip the tutorial, but through the game creation process.
Maybe having the vanilla as the recommended option with the points system unlocking after one playthrough?
I don't think the balance is a huge concern, it's a sandbox and if you want to cheese it, you will always be able to. This would just make for interesting playthoughs without the extra busywork at the beginning, like setting all factions to negative opinions or going full merchant.