Maybe having the vanilla as the recommended option with the points system unlocking after one playthrough?
Hmm, perhaps. I think the setup for forcing you to play the campaign tutorial first time works on something like this, and has a reference of some kind in the rules.csv. Could bear a little research.
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.
I thoroughly disagree with this. If you want to be able to pick from any and every ship, weapon and then screw around with faction relationships, you're looking at the wrong mod.
I hold balance in extremely high esteem. Sure, Starsector is somewhat a "sandbox" game in the sense that it's a story-less open world game. That doesn't mean balance isn't relevant. If anything it makes it
more important because there are no missions or stories or quests that the player does in a particular order that would otherwise affect their progression. You start small and weak, you have awesome adventures and epic battles, and you get bigger and stronger - that's the point of Starsector IMHO. If you were to start the player with top-end stuff, suddenly there's no progression whatever and you're just flying around stomping stuff.
If that's the way you prefer to play, then I can't argue with that, but once again this is not the mod for that. Better Beginning's objective is just to add a little more variety and focus to the ship selection at the start of a game. Sorry, but that's the way it is. If you want to cheese the early-game, I can only point you in the direction of Console Commands if you haven't already tried it.
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.
Contrary to the above, this
is an objective of this mod. As yet I don't know how to change faction relationships, but suggesting more specific roles for your game is definitely something I want to encourage.