I'd say Vanilla isn't exactly hard to make progress in once you figure out the way things work, I've owned SS for a little more than a week and yes, got to your point pretty fast, but here's the deal, you can roleplay and limit yourself, also, don't be shy of annoying other factions, it may look like the way to go, but it renders the game flat after a while.
I'm currently trying this:
- A pirate playthrough, trying to get my rep up with the pirates, at the expenses of every (or almost) factions. Making money by smuggling and having to constantly avoid factions patrols is quite challenging.
- A merchant playthrough with a fleet mostly composed of freighters, basing your decision making on the economy. You'll have to be very careful of pirates and enemy factions, minmax your logistics, fuel costs and such aiming for the best possible profit. Also, trading with a faction ruins your rep with the opposing ones, which makes room for more meaningful choices.
Other than that I'd say get into modding. SS+ may be the way to go. Get that and a bunch of cation mods and the game will feel completely new.