That'll take them another decade of development with 1,000 planets.
Yeah, I suppose the scale of the galactic map would have to be reduced. It seems like a fawlty design philosophy decision right from the start, honestly - I wonder how many people are actually enjoying the No Man's Sky aspect of "there's 9999 trillion planets (that all have nothing on them)!!!".
Getting licenses to fly better ships should just be quests. Not something you build your character around. Of course everyone will want better ships. Skills dedicated to being a better more efficient pilot are fine as skills though.
But then my character and your character would both be able to fly the best ships, even though I've invested in (say) social skills like persuasion and diplomacy and you've invested in (say) science and crafting skills. Both of our characters would inexplicably be ace pilots, despite the fact that I'm theoretically a diplomat and you're theoretically a scientist.
Anything that differentiates character builds, and makes it so that the person you're playing as isn't an expert at everything and has both strengths and weaknesses, is good in my book.