I mean, seriously, the story can get in the way of your own story, but some people seem to enjoy the story for some reason. If you are really focused on trying to please everyone, why not turn the story into a dev-made mod? Since the philosophy of being mod-compatible is "If you don't like the game, add more mods" and modding the story OUT of Starbound is proved to be an irritating task, changing the story into just an addon that you can disable at any time would give the players a lot more freedom. Now you're probably asking "Well, if the story isn't there, how do you fix your ship?" Easy answer, make the core fragments one of the parts to fix your ship like in Glad Giraffe, make the outpost a selectable coordinate when this is done and finally, just have Pete sell you the crystals. There, story averted. The dev mod would simply add in Esther, remove the option to buy crystals and drop the Very Plot Relavent Gate into new garden planets when you load them with the mod. This will however, cause an issue if you go into a world where you haven't gone to the outpost with the mod activated and said world was created before you activated the mod. This could just mean that that particular world must be played with the mod disabled. Though for vice-versa, the plot things could just be left buried somewhere in the game's assets. This would allow anyone to disable and enable the story completely at will. And that's my peaceful answer to this issue.