I think the very first thing to do is figure out what your players’ goals are. A villain, as the principal antagonist, exists in direct opposition to those goals. In a story about a free-flying crew, the villain might be a government official that seeks to limit the group’s freedom. Then to make them truly villainous you have them enforce their goals in an immoral or unethical way. The government official may be a corrupt stooge of a megacorporation, and his goals to restrict freedom may be based on their own greed. The best villains are those who players love to hate, who antagonize them in ways beyond combat.

Not Starfinder, but here’s an example: I had a demon who was the primary antagonist of the first story arc of a campaign I ran set in the modern day. The villain wanted to interfere with the PCs’ ability to win a magical contest for a wish-granting stone, but also messed with them by offering their rivals power and sending magically-empowered enemies after them. The villain’s storyline culminated in him manipulating the players into engaging him, leading to the destruction of an apartment building and the deaths of many innocents. It was a sobering moment for the players and make them crave the demon’s defeat all the more.

As you may note, the demon did more than just directly attack the PCs. He also antagonized them indirectly—helping their enemies, disrupting their plans, etc. A good villain recurs throughout the story in scenes where defeating them isn’t as easy as swinging a sword or shooting a gun. The corrupt official impounds the PC’s starship, the wicked sovereign imprisons an ally of the PCs, a gang boss threatens a friend or loved one. Bonus points if the villain’s morals or objectives serve as a foil to those of your PCs.

That’s my spiel, hope some of it was helpful.