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So, in Zirakinbar's excellent 'Of Clones and Wizards', linked above, we are treated to the concept that the Sith started out as Hermione Granger's brainchild, an effort to bring about an end to Grindelwald's subjugation of muggles. Basically, with Harry having been sucked off into a distant future in Star Wars, the wizarding world's war against Voldemort went very badly and after Dumbledore was killed they pull Grindelwald out of mothballs to save them. After he does, he starts using magic to literally compel muggles to behave the way he wants, so Hermione and the others break magic, turning it from Harry Potter magic into the Force. She names her group S.I.T.H. - Society for the Integration of the Totality of Humanity, and they are vilified (so this alternate history shows) in the aftermath.
(If you like Harry Potter, you should totally give it a whirl, it's a great fic, though unfinished)
Now, here's the thing, I can easily see how the modern Sith developed out of Hermione's movement, while the modern Jedi come from Grindelwald. It's actually very simple. If you tell everyone that the Sith are the bad guys, then you're going to get a whole whack of bad people who want to join up, and declaring the Jedi the good guys means good people want to join up there. Give it a few centuries and the two would have switched sides.
Which brings me to my idea.
The starting point is that way back in history, the Sith were passionate Force-sensitive do-gooders. They did occasionally 'fall to the dark side' so to speak, but basically, they were all about getting out there and doing stuff to help people. The Sith code thus has its roots in a philosophy of avoiding complacence.
The Jedi meanwhile, were exactly as bad as those who are their detractors like to say. They were holier-than-thou, actively worked at being emotionless, and put themselves at the beck and call of the status quo, attempting to shore up whatever was deemed to be most orderly, whether or not it was good. They were an evil masquerading as good. You know, Order at the expense of every single other good thing in the galaxy.
Over time, bad press started to dog the Sith, and they started getting more people joining the Sith who were there to spite the Jedi, rather than to do good. They got people who believed the Jedi's press releases claiming the Sith were the bad guys.
Meanwhile, more people joined the Jedi, under the impression the Jedi were the good guys, and effectively the Jedi changed by grass roots movement in the same way the Sith did.
Millennia pass, and now the Sith are mostly Bad and the Jedi mostly Good and no one remembers the origins, because everyone believes the bad press that was sent around by the Jedi back in the day.
There are still good Sith, hovering around in the background, but you don't hear about them, because they weren't empire-building and learned not to tell anyone that they were Sith.
Now, there is a line of canon that states that Anakin is not a child of the Force, like he was Jesus or something, but is instead the result of Darth Plagueis doing experiments in creating a kid with more midichlorians than anyone else. So, let's say that one or more ancient holocrons from ye olden days of good Sith, maybe even some other Sith artefacts so old that no one can read them as being Sith manage to work their way back to Tatooine with Shmi. I mean, all kinds of stuff happens because of the Will of the Force or the Will of Force Objects That Want Something.
When Anakin and Shmi get sold to Watto, Anakin finds those holocrons that had been refusing to open for the Sith for millennia, because those Sith were evil, and these early Sith are not.
The holocron(s) opens for Anakin, and they become his mentor(s). Now, they're old, delicate, don't always work as well as they might and can't teach Anakin hands-on the way a proper master could, so they're always on the lookout for someone who could teach him.
So, when Qui-Gon shows up, even though these ancient Sith are leery of the Jedi, they figure that Anakin can get all that practical training from a Jedi. Anakin leaves with them and Phantom Menace goes ahead. However, because Anakin has been trained by a good Sith for years now, when he's facing the Jedi Council, he's not scared because he's got his holocron teacher/friend(s) with him, he understands at least some of what the Force is about, and he can better read Force currents in the room, and basically just has more of a sense of understanding and control about what's happening.
Either that, or when they get after him about being scared, he doesn't try to bluff, but instead at the prompting of his holocron buddies through a Force bond says (as has been pointed out in many a fanfic), "I'm thousands of lightyears away from everything I know, I'm cold, you're all looming over me and judging me and acting like you're fundamentally better than me and I don't know if you're going to throw me out onto the street after this, so I don't know if I'm going to have to find work just to survive on this planet."
Anyhow, the point is, instead of saying they're not going to take him at all, they say that he's traditionally too old, but with his midichlorian count they have to think about it.
Basically, we're reducing the initial friction between Anakin and the Jedi by making it a maybe instead of a hard no-because-you're-clearly-going-to-be-evil (or at least, that's how Anakin thought they felt about him in the movie).
When Obi-Wan starts teaching Anakin, his training is supplemented by the holocrons. This makes Anakin both better at being a Jedi, but also they are ancient and biased against the Jedi, due to the Jedi having been emotionless government stooges back at the beginning of time. Anakin actually winds up having to argue with the holocrons in favour of the Jedi, because there are things the holocrons think that are patently not true in Anakin's real life experience.
He also argues with the holocrons about Palpatine, because they think something is hinky.
As Anakin gets older, having a Sith-when-Sith-were-good mentor really just gives him a balanced perspective and here is where there's a lot of freedom to Jedi-bash if that is where you want to go, or you can have the Sith-when-Sith-were-good be happy to discover the Jedi are now good guys and be even more depressed about how bad the Sith have become.
I am also somewhat imagining that when the war starts the Sith holocrons tell Anakin to go break into the vaults with the older Jedi holocrons that date back to when the Jedi had the Army of Light and ask for advice about being a general. At this point I am also torn about Anakin walking off with a new Jedi holocron friend who is very salty about the people they're getting along with best is a Sith, or else the Sith being salty about Jedi holocrons not being real people anymore.
Anyhow, with all the times Anakin and Obi-Wan face off with Sith, Anakin winds up getting lessons in being a good Sith, which makes him do super-well at handling the Sith. Maybe even managing to effectively get Ventress away from Dooku because one of his holocron buddies decides to take off and hang with her. She winds up deciding to just take off and start up a new Sith temple in the style of these super-ancient Sith because the Rule of Two is megalomaniacal nonsense.
Heck, maybe that time Anakin, Obi-Wan and Dooku are all held captive by Hondo, Anakin basically talks Dooku around, because in theory he went to the dark side to make good reforms to the galaxy, and these ancient Sith holocrons offer him an out to create a new Sith temple in the ancient idiom. So he and Ventress abandon the war and go on Search for Force sensitive kids to raise in the ancient Sith idiom.
Then the war falls apart because Palpatine doesn't have anyone on the other side directly working for him like Dooku, so he has no way to run the war from both sides. That means that suddenly all the info going to the war effort on the Republic's side is genuine, and the Separatists aren't being sabotaged, but at the same time, no one is undercutting efforts to make peace from both sides. So the war ramps up, and then abruptly ramps down as people suddenly realise how badly they don't want this war anymore. There's only so much needling Palpatine can do, and without someone he can give explicit directions to on the other side, he has way too little control to force things in the direction he wants to.
At some point Palpatine is exposed and someone kills him and then Yoda and the rest, after examining the values of the super-ancient Sith realise the Jedi were the bad guys umpty-squillion years ago, just with better publicity, and the Sith and Jedi reach a sort-of truce with the Sith handling the outer rim with a more active sort of handling, since it's more of a wild west out there, and the Jedi handle the Mid-rim and Core where slicker political types are needed.
And Jocasta Nu leaves the Jedi and moves out to hang with the Ancient Sith because a primary resource is a primary resource and she's just going to do archaeology.
Or something.