I have always loved the prequels in spite of their flaws, but I grew up with them. Probably the most appealing thing about them for my friends and me was the worldbuilding to the universe, not just from the trilogy but also from that era of Star Wars content that it kicked off in general.
The two worst flaws of the prequels in my opinion are the depiction of Anakin and Padmé's relationship dynamic on-screen and the lackluster scriptwriting in general.
For the former, I disagree with the most prevailing criticism of Padmé "condoning" Anakin's massacre of the Tusken Raider tribes because in the context of that particular moment (Padmé was anxious all night at both Anakin and Shmi's wellbeing), of their relationship (she actually saw him as a real friend who she cared about), and Padmé's personality (a martyr complex who struggle with boundaries), it is not at all realistic to expect her to ghost Anakin right then and there. The problem is that the movie does not present the canonical dynamics of their relationship well to us due to poor editing decisions that truncated their dialogue, poor acting direction, and poor chemistry between the actors, all leading to the film telling us that Anakin creeps Padmé out and then she suddenly falls in love with him anyways. That is apparently not the narrative intent as clarified in the novel, which is that Padmé was already attracted to Anakin when they first met again as adults, had an emotional need that he could fulfill, and that they both felt conflicted. The fact that Attack of the Clones pretty much portrayed the opposite is its most substantial flaw... but for me, it is a testament to its other merits that it is still a good movie overall.
I think their romance tends to overshadow those other merits, like all the incredible work that went into the cinematography, the world design, and the sound design, or how the plot in general is concise, well-paced, and fits into the overall saga. If you rewatch some scenes in isolation, like the pursuit of Zam Wesell, the fight between Obi-Wan and Jango on Kamino, and the subsequent dogfight over Geonosis, Attack of the Clones has some truly amazing cinematic scenes.
For that matter, there is nothing wrong with Palpatine's assassination attempt of Padmé. His aim was to eliminate the leader of the opposition to the Military Creation Act, and hitmen subcontracting to other hitmen is true to reality (there was a funny story that came out of China once where hitmen kept on subcontracting the hit until like 8 rounds later the last guy felt that the cut wasn't worth the trouble and reported them all 😂). Jango Fett using a dart he thought would be untraceable is a genuine and realistic tactical mistake, which the Visual Dictionary published at the time already addressed in the form of a dispute with Zam Wesell about the stealthiness of the attack vs. leaving behind evidence.
As for Revenge of the Sith, I wholeheartedly believe that it was a 10/10 across all metrics except the fight choreography (of Anakin vs. Dooku & duel vs. Sidious) and the dialogue, which was pitifully weak and dampened (but did not ruin) the emotional impact of some critical scenes like the duel on Mustafar. Unfortunately, dialogue is a huge part of what makes or breaks a movie, and again, it is a testament to the strengths of the film that it was not ruined because of the terrible lines. It has what is in my opinion the best opening cinematic out of every film in history, as well as one of the most creative plot twists (Order 66) that we now tend to take for granted.
Anakin's fall to the dark side is very profound, and he is one of the most well written characters in fiction in my opinion. I notice a lot of people miss the complex psychological issues that led up to it, like his inability to confront his own mistake of getting Mace Windu killed, the egotism behind his love for Padmé resulting ultimately in domestic violence, and his underlying tendency to devalue the lives of people in his out-group.
As for The Phantom Menace, my issue with this movie even back when I was a kid is just that it is relatively boring. It is a plateau the entire way, and I never hit a high watching it. Only the climactic duel with Darth Maul comes close. Even reading the novel, I felt like I was reading one of those boring Scholastic novels back in elementary school. But boredom aside, the plot is genuinely okay. There aren't critical lorebreaking problems with it unlike with the sequel trilogy.
Finally, I also never understood the criticisms of the CGI beyond that it was challenging for the actors. The CGI of the prequels was actually groundbreaking for their time and are better than a lot of the CGI in recent Marvel movies and Star Wars shows.