Obi-Wan Kenobi is one of the two main protagonists of the Prequel Trilogy and is not known to be a blood relative of the Skywalker family.
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Also, praise the Sequels for making Rey not a blood relative of the Skywalkers all you want, but if the Sequel Trilogy does anything for the eugenics implications I'd say it strengthened them - Kylo Ren's the third generation of powerful Force adepts out of the Skywalker family, and Rey just so happens to be a powerful Force adept who's the granddaughter of another powerful Force adept. This is reinforcing a pattern that says that Force sensitivity is a heritable trait, not weakening that particular implication. Additionally, whereas the Original and Prequel Trilogies indicate that great potential is not particularly meaningful without training and dedication, the Sequel Trilogy simply hands Rey powers with seemingly no justification other than who her grandfather is, which is significantly worse in terms of what it implies for a hypothetical eugenics program than just making people from the 'right' families have higher potential.
The Prequel Trilogy is much better than the Sequel Trilogy in terms of eugenics implications:
- Skill and experience trumps strength in the Prequel Trilogy: Anakin loses to Dooku and Obi-Wan despite The Phantom Menace indicating that he has the highest Force potential of any known Jedi. By contrast, in the Sequel Trilogy Rey's a better Force user than Kylo from at least the point where he tries to interrogate her despite Rey being entirely untrained, and she also beats him in every fight they get into.
- Anakin is the only "protagonist-level/antagonist-level" Force adept from a 'special' family in the Prequel Trilogy; Qui-Gon Jinn, Obi-Wan Kenobi, Darth Sidious, Darth Maul, and Count Dooku are unrelated to the Skywalkers as far as we know from the films. By contrast, Rey is the granddaughter of Emperor Palpatine, Kylo Ren is a Skywalker, and Snoke is apparently something Palpatine created in a test tube.
- The Prequel Trilogy has by far the highest incidence of Force adepts who are not related to the Skywalker family or any other known Force adepts. Sure, most of them are barely deserving of the 'character' in 'background character,' but they're still there. The Sequel Trilogy - fan theories about Finn aside - only has Temiri Blagg, who isn't any more of a character in The Last Jedi than, say, Eeth Koth or Plo Koon are in the Prequels.
- If the Jedi Order represents a reasonable fraction of the galaxy's Force sensitive population, then the Prequel Trilogy shows that there are far too few of them for Force sensitivity to be a simple matter of genetics - there's only ten thousand or so Jedi in the waning days of the Old Republic whereas Coruscant alone probably has a population in the trillions.