The villains of the Star Wars prequel trilogy are each a part of Darth Vader, heralding Anakin Skywalker's tragic turn to the dark side. Unlike the hyper-secretive Star Wars sequel trilogy, George Lucas was very open during the production of Episodes I-III given that their endpoint was so well known. Set videos were released online regularly, and there was a lot of dramatic irony inserted into the films themselves - perhaps more than anybody realized.
Whereas the original Star Wars trilogy had Darth Vader and the Emperor its overarching villains (with support from Grand Moff Tarkin, Boba Fett and Jabba the Hutt), the prequels had a revolving door of baddies. The Phantom Menace had Darth Maul, Attack of the Clones Count Dooku and Revenge of the Sith General Grievous, each of whom played a part in commanding the forces of the Trade Federation and later the Confederacy of Independent Systems. Of course, this was because the real villain - Palpatine aka Dark Sidious aka The Emperor - was pulling the strings in the background throughout, with his lackeys killing time until "Chosen One" Anakin Skywalker took center stage.
But Messrs. Maul, Dooku and Grievous weren't just fun merchandisable diversions (at least mostly). One reading of the villains (via Reddit) suggests that, together, they represent a different side of how Anakin Skywalker will fall to the dark side, grim foreshadowing of his tragic fate.
Darth Maul is an interesting case as who this character is has - like Vader - evolved so much since his introduction. In The Phantom Menace, Maul was a simple Sith apprentice, a near-silent fighter of pure rage as a boss fight for the Jedi. However, after multiple non-canon resurrections, he was officially brought back in The Clone Wars as a more calculating figure driven by revenge - first against Obi-Wan Kenobi, then his former master, Palpatine. Both sides capture the motivation that drove Anakin to the dark side and would go on to justify Darth Vader's atrocities.
Count Dooku is perhaps the most underserved Star Wars prequel villain given his stature - a key role in two movies and prime antagonist of a TV show yet he doesn't even have a canon first name - but what he represents for Darth Vader is unavoidable. He's a fallen Jedi corrupted by Palpatine who strikes at their heart. It's not too well shown in Attack of the Clones thanks to a malnourished is-he-isn't-he-evil "twist", but he highlights how even the greatest are susceptible to the dark side; as Yoda's pupil and Qui-Gon's master, he's a one-generation gap between the head of the order and the one who pushed to find Anakin.
Finally, as a machine-masked cyborg with a breathing defect, General Grievous is the most obvious parallel and the one that George Lucas has most openly discussed. The droid general is distinct from the other prequel villains in how he's not a Sith or Force user (he does have a fine lightsaber collection though) and is dispatched at the midway point of his movie. But that shouldn't sidestep how he's clearly intended as a show of what Anakin will become, menacing but not whole, superior yet permanently injured; there's even a hint of contempt in their first meeting in Revenge of the Sith that becomes heavily ironic by the movie's end.
The similarities are compounded by their deaths. Two involve dismemberment, two are at the hands of Obi-Wan Kenobi, Grievous is engulfed in flames and, admittedly after the fact, one - Maul - came back as a cyborg. Part of this will be Star Wars' propensity for similar modes of death - five limbs are cut off in the original trilogy alone - and Obi-Wan's dominant role in the prequels, but taking into account everything before, there's some rather overt foreshadowing of Anakin Skywalker's ultimate fate.
Whether or not this was intended by Lucas - a distinct possibility given his interest in storytelling that rhymes (see also: Ring Theory) - or is merely a by-product of franchise tropes, it does go to show that there's more to the Star Wars prequels than many like to admit.