The “Darth Vader hunts down and terminates Jedi” movie sounds cool in concept, but would probably be hard to write in a compelling way. You’d need to establish the characters of Vader’s victims - and you can’t even use Obi-Wan as one of them. And as the third movie in a Trilogy, there’s just not really enough material that ties back into the pre-Vader story lines (stuff from Episode 1 and 2, like the Clone Wars, etc.) that also overlaps with a post-Vader Episode 3 murder-fest story-line. I think a story about Vader hunting down Jedi survivors would potentially be easier to implement as a series instead of a single movie, as it would necessarily require establishing new characters who are Vader’s victims before killing them off.
The real gold that could have been mined from the Prequels was the relationship/friendship between Anakin and Obi-Wan and Anakin’s heart-wrenching betrayal of his mentor and best friend. But bizarrely, that was barely explored in Lucas’ Prequels.
Are you really saying that there isn’t enough time in two whole movies to establish new characters worthy of being hunted down by Vader in a third movie? Because I’m pretty sure two movies is more than enough time (seeing as the vast majority of movies have to set up and payoff characters/plotlines within a single film and aren’t part of some bloated trilogy). And you say “there’s just not really enough material that ties back into the pre-Vader story lines (stuff from Episode 1 and 2, like the Clone Wars, etc.).” I think you’re missing the point. We wouldn’t be filling those first two movies with existing material from the current prequels/clone wars cartoons. We would be making two entirely different films and filling them with brand new stories/subplots/characters (with some old regulars, of course) which would set up the events of the third and final film (which wouldn’t be made up ENTIRELY of Vader’s rampages; i.e., the film wouldn’t be just one long hallway scene, but would be the culmination of all the various subplots and arcs set up in the previous two movies (which would now include all of the Anakin/Obi-Wan friendship/betrayal dynamics you mention that are indeed underexplored in Lucas’ prequels) with an admittedly heavy dose of hunting down the remaining Jedi and other threats to the Empire).