The part about being born of no father is what ultimately convinced Qui-Gon that Anakin was the Chosen One, because Anakin's mother Shmi Skywalker had told Qui-Gon that Anakin was born through immaculate conception.
Qui-Gon Jinn was certain of Anakin being the prophesied 'Chosen One' because this young slave boy from Tatooine ticked every box in the Jedis long foretold prophecy of one who would bring balance to the force. His number one tell-tale sign was Anakins midichlorian count, being more than 20,000.
Qui-Gon sensed the living Force at work when his diplomatic mission to Naboo failed and he was forced to accompany Padmé Amidala to the Hutt-controlled world of Tatooine. There, he discovered Anakin Skywalker, a boy with enormous strength in the Force.
Luke's resolve was that he would help redeem his father, or die trying. This is why some people believe that maybe Luke was the Chosen One, but, in actuality, it was Anakin who destroyed Darth Sidious; and he destroyed Darth Vader when he chose to exchange his power for the love he had for his son.
Summary. Qui-Gon saw potential in young Anakin Skywalker as the Chosen One, and could have prevented his dark fate. Marvel's new Phantom Menace Special issue further confirms Anakin needed Qui-Gon's guidance to control his emotions and remain on his Jedi path.
Thus, while Qui-Gon was less powerful than the likes of Yoda and Mace Windu, Palpatine feared him more. In the simplest terms, he was a wild card, and with the Sidious executing an intricate decades-long plan to seize power and destroy the Jedi, a wild card was something he just couldn't afford.
What would have happened to Anakin if Qui-Gon lived?
Had Qui-Gon lived, however, he would have become the father-figure Anakin so desperately needed. The bond between Qui-Gon and Anakin would have been far greater than simply master and apprentice; they'd practically have been father and son.
The Chosen One was revealed to be Anakin Skywalker, who conceived by the Force itself via the mystical one-celled organisms called midi-chlorians completely without outside influence.
In order to cement this idea, he revealed Anakin Skywalker was the Chosen One, a mysterious being with a unique destiny. This added a new Messianic element to the Star Wars franchise, with Anakin considered a human vergence in the Force.
Darth Vader's true identity as Anakin Skywalker was a highly guarded secret, known only to a select few individuals including Palpatine, Obi-Wan Kenobi, Luke, Han, Leia, R2-D2, C-3PO, Master Yoda, Bail Organa, Ahsoka Tano, Darth Maul, Grand Moff Tarkin, Grand Admiral Thrawn, Jocasta Nu, Ferren Barr, Verla, Reva, ...
Master Qui-Gon Jinn's words echo in Vader's mind. There's no anger, nor hatred in this memory – Vader simply recalls one of the first lessons the Jedi Master slyly gave to young Anakin Skywalker.
Did Emperor Palpatine know that Darth Vader was Anakin Skywalker before he revealed it to him? Yes, of course. Palpatine had known Anakin since childhood: “We shall watch your career with great interest”.
Count Dooku's real name, Dooku, was more fitting than his Sith title, Darth Tyranus, as it speaks to his manipulative nature. Dooku played a crucial role in weakening the Jedi and the Republic from within, planting doubt and eroding trust.
Legend had it that Yoda—a Jedi who became Grand Master—was trained by N'Kata Del Gormo. A Force-sensitive Hysalrian, N'Kata Del Gormo was trained in the ways of the Force and achieved the rank of Master within the Jedi Order.
Qui-Gon was Dooku's apprentice. Dooku loved Qui-Gon like a son due to their many similarities; both were individualists, idealists, and both had knowledge of the Force that was unique.
Going by potential power Anakin has 20,000 midichlorians that is known of, but his full potential could have been much higher, maybe 30,000–40,000. Palpatine is stated to have 19,000, so I would safely assume that Rey could have anywhere from 12,000–15,000.
In an early Revenge of the Sith draft, Palpatine confirmed that Darth Plagueis used the Midi-chlorians to start the cell division that created Anakin Skywalker.
The realistic answer seems to be, yes, Anakin in his prime could have defeated Luke Skywalker (in the current canon) if they battled one-on-one. The main reason behind this is Luke's lack of formal Jedi training, at least when it comes to combat.
Who was the last Sith the Jedi knew about before Maul?
Almost 1,000 years after Bane's death, Darth Plagueis trains Darth Sidious, who ultimately kills his master and takes Darth Maul as his first apprentice. Star Wars: Episode I – The Phantom Menace - Sidious and Maul are the only known Sith in the galaxy.
Darth Maul and Qui-Gon Jinn's duel on Tatooine in Star Wars: Episode I – The Phantom Menace revealed the Sith Order's survival to the Jedi after 1,000 years of secrecy, with Jinn somehow concluding that Maul was a Sith Lord.
Dooku, AND Anakin, would be less likely to fall to the dark side if Qui-Gon was left alive and Maul's sympathetic past would never be revealed. For the former, Order 66 wouldn't be executed since Dooku wouldn't be the one planning to do that on the clones.
Unlike in the movies, the Jedi Order would still be around to help each planet restore balance after their respective conflicts and to maintain peace in the years that followed. Palpatine's plan to install a Galactic Empire would come to a sudden halt and the Republic would be allowed to continue as it always had.
As the Chosen One in his prime, it's quite possible that Anakin would have had a strong chance of defeating Palpatine aka Dark Sidious. Palpatine himself told Yoda before their Revenge of the Sith duel on Coruscant that Darth Vader would become more powerful than either of them as he continued to grow in the dark side.
