What sabotaged the prequels in a larger sense is that Lucas had no adult supervision since he was not working for a public corporation with shareholders and a board of directors to answer to, who could have kicked butt if substandard movies were made that underperformed.
The Empire Strikes Back and
Return of the Jedi were both independent productions produced by Lucasfilm.
Star Wars, on the other hand, was a studio picture, and by all accounts Lucas had to fight with the board of Twentieth Century Fox tooth and nail to get the film made, and to get it made his way. (Thankfully, he won).
What the prequels didn't have was a producer like Gary Kurtz (IV, V), a screenwriter like Larry Kasdan (V, VI), or a director like Irvin Kershner (V) -- people who could disagree with Lucas or at least present another point of view.
A board of directors would have likely looked at the box office receipts of
The Phanton Menace and put as many sequels into production as possible (which, lo and behold, is exactly what Disney is doing now that they control the property).