As far as the Prequels are concerned, I think that, given time, we would get an alternate take on the Prequel Trilogy and Anakin Skywalker’s story after the conclusion of the New Jedi Order series, as to not complicate things lore-wise during production. Once that’s wrapped up, I believe that’s when authors and other executives will turn their attention to create a project dedicated to telling the full story of the Clone Wars, the fall of the Republic, and Anakin’s transformation into Darth Vader. It would be like the Clone Wars Multimedia Project, but it starts at the very beginning of the alternate PT’s story and goes from there, expanding Anakin and Obi-Wan’s characters while introducing new characters that are connected with already-established material. I believe the Clone Wars here would follow something along the lines of Timothy Zahn’s envisioned version of the Clone Wars, while taking some artistic liberties of cut content from decades prior (such as the scrapped Kenner toy-line with Atha Prime). We would see Republic soldiers against enemy cloned warriors in a war that would last for many years, devastating the galaxy and whittling the Jedi Knights’ numbers over time. Whether or not the Jedi are destroyed during or after the war’s conclusion is up in the air, along with how quickly the Republic transformed into the Empire. The authors would probably try to focus on what the films set up first with backstories (Anakin and Owen’s brotherhood, Obi-Wan convincing Anakin to leave Tatooine to fight in the war, etc.) and then the rest is filled in with EU stories (some of which are quickly rectified to avoid continuity problems). Plus, the Jedi would be allowed to marry and have families; in fact, I reckon we could see some GoT-style conflict between Jedi dynasties and their views on the Force, Clone Wars, etc. It could even pave the way for a Jedi civil war but set in the Clone Wars era, with the survivors later hooking up with Palpatine’s Inquisitors or going into hiding
As far as the NJO is concerned, had Lucas decided to give the keys of the franchise over to EU authors, I believe Star by Star wouldn’t have killed off Anakin Solo and things would progress from there. The Solo Kids would reunite and lead the charge to retake Coruscant from the Yuuzhan Vong, each sibling goes off on their own path to find their calling (Anakin to become Luke’s successor, Jacen to explore the mysteries of the Force, and Jaina to continue being the “Sword of the Jedi”) and the post-Endor stuff would conclude there. If not, then it would probably focus more on the recovery aspect of the galaxy following the war’s end or Jacen’s journey to learning about the Force while Anakin and Jaina deal with some small crisis back in their galaxy. Without the PT films, most of the stuff the post-NJO had to work off of (Dark Nest with the Padme subplot, LOTF with the Mando shit, and Legacy comics with Krayt’s backstory) would result in a massive change and/or overhaul of plans following this.
As far as the post-Tales of the Jedi Old Republic is concerned, I think that without the PT films, KOTOR’s aesthetic would follow more of what we see in TOTJ. I think the story would remain the same, however, regarding Revan and Malak. SWTOR would also have the aesthetic change thing, and the Bane books would remain the same. However, I think that the Darth title would have been introduced in the Bane books themselves, as well as the rule to have a red lightsaber. But before the Bane books, I think the Sith would have been depicted the same way they’re depicted in TOTJ.
Overall, I think this would be a better universe for Star Wars as a whole, as the fandom would be more united. Instead of having OT fans against PT fans against ST fans against EU fans against Canon fans, we would only have film purists against those who accept both the films and the EU. And that’s it. There wouldn’t be as much division as there is today.