Plot-wise, the biggest problem here is that you remove the singular Act that completed Anakin's fall to the dark side.
In fact, this may even cause Anakin to Not fall.
Yeah, this would completely undo any gains the Sith make by showing Anakin their true colors. For all the faults of the Jedi Order, in this scenario, they'd be infinitely more tolerable for Anakin.
Anakin sticking to being a Jedi and potentially gaining full mastery of his powers is a complete disaster for the Sith. The man is a living god, in fact, he's so powerful he can't meditate properly at all. Seriously, it's not that he's impatient or undisciplined*, but when he meditates and taps into his connection with the Force...
...Anakin outright describes it as like looking into a supernova. Something reinforced by the events on Mortis, with Anakin's brief tapping into his full potential allowing to simultaneously subdue the literal embodiments of the Light and the Dark.
Of course, you could say the Sith should just make sure never to engage Anakin directly or at least without setting up beforehand...except Anakin is also one of the best field commanders the Jedi has. Enough that despite Tarkin's general disdain for the Jedi, he quickly and genuinely learned to respect Anakin once the latter proved his command ability. Sure, he's heavily offense-oriented, and likes to take risks, but he gets things done and has the love and respect of his troops**. Put him in with the Rebel Alliance, and he can make life so very difficult for the Sith they may have no choice to face him directly.
I really, really doubt any Inquisitor would last very long against Anakin. That, or they turn into Saturday morning cartoon villains/Team Rocket expies, only thanks to Anakin not particularly inclined to kill them because of how pathetic they are. You'd need a full-fledged Sith Lord to have a shot against him, and the more experience he gets, the wiser he grows, and the more comfortable he is with his powers, the smaller their chances become. Past a certain point, I suspect Anakin could face Darth Sidious, and potentially simply snuff out the latter's power and force him to his knees with a simple gesture, much like he did to the Avatar of Darkness on Mortis.
*Anakin
is impatient and undisciplined, but that's only in the general scheme of things. He's patient and disciplined enough to have a level of lightsaber skill that's comparable to High Councilors despite only being a Knight. In fact, AFAIK when it comes to lightsaber skill, he's one of three people capable of not losing to Darth Sidious, something only Windu and Yoda are capable of.
And in another hit or miss case for Disney Star Wars, Rebels actually reinforces this with that training hologram of Anakin teaching Form IV lightsaber techniques. How, you ask? Form IV is weak against blasters and/or multiple opponents...except Anakin's variant of Form IV was able to make up for those deficiencies, something (Legends) Yoda explicitly mentions only a full-fledged master of Form IV is capable of.
Anakin/Darth Vader only lost to Kenobi on Mustafar thanks to being unused to the Dark Side of the Force, causing him to become even more reckless than usual. As shown by his record in following decades (at least in Legends), Darth Vader was able to compensate for his crippled state, and by the time he met Kenobi again, simply overwhelmed him.
**Hell, he kept this even as Darth Vader. The officers might fear and tread lightly around him, but the rank-and-file just loved Darth Vader, as his willingness to fight on the front lines proved his high standards weren't just him being a martinet. His high standards were all based on actual experience, and his willingness to risk his life next to the boys in the trenches meant they didn't mind chasing after those high standards. That, and Darth Vader typically held officers, not the men under their command, responsible for any failures.
