I'm surprised no one mentioned this one. Space Pirates and Zombies.
One of my favorite games to date. So far i've played/beaten it 3 times.

I think this is what you are looking for:
Starsector
SsethTzeentach review

The reasons are that I haven't played Starpoint Gemini 3 and that Warlord is just ok IMHO and not as good as 2.

Edit:
SPAZ 1 and 2 could be also interesting for you.

Nexus: The Jupiter Incident is on GOG and has an amazing story line. You both level up your crews and upgrade your ships. Not a very open world though. It is missions based and linear.

Escape Velocity: Nova is an old shareware game from Ambrosia SW that was an open world where you could be a trader, pirate, Rebel, etc. Tons of customization and user mods. Unfortunately, Ambrosia ceased existing a few years ago, so I don't know how you would get a copy now. There is a Kickstarter for a remake of an earlier iteration of the game Cosmic Frontier: Override which looks promising.

Wing Commander: Privateer, Privateer 2, Rebel Galaxy, Everspace, Elite: Dangerous, Spaceforce: Rogue Universe, Darkstar One, Galaxy on Fire 2.

Gravity Well rocks but it isn't an RPG and I think there aren't many people that have the patience for it. Haxus doesn't sell it anymore and he isn't working on Hazeron either.

I forgot to mention Endless Sky in my list, and I don't want to edit this late.

Let me add Freelancer to this nice list :-)

Yeah, it did rock. It's part of the reason why I wish GOG would peruse the library of old shareware. There's good gems that could just use a slight clean up and pop, you've got something cheap for sale!

Gravity Well 6 failed. I think I was pretty much the only one that paid for it. It also needed to connect to a server even for singleplayer. 5.2 was the last version that didn't. There's a small chance that GOG could get 5.2 but I don't think they'll bother.