TPM’s only advantage over the other two is Darth Maul really. Honestly whether it’s better or worse than Clones depends on whether I’m in a mood in which I find Jar Jar or sand romance more tolerable, but I think ROTS is a huge step above both. Phantom Menace’s greatest crime in my view was just that it’s sooooo boring. Pacing was just awful. Even Jar Jar could have been tolerable if it was fun to watch. But the movie stops dead in its tracks for a loooooong detour on Tattooine before it picks back up. Clones had the same problem to a lesser extent; at least the Obi-Wan subplot was kind of fun and at least there was some sort of emotional impact with the sand people and Anakin’s mom. Phantom Menace didn’t have any of that. It was just pod racing and Watto and kiddie Anakin running around for like 45 minutes that felt 10 times longer. So it’s probably my least favorite for that reason, though sometimes I do prefer it to Clones.
Eh not really. TPM has many practical effects, miniatures, sets, and some CGI that still holds up almost 20 years later. It was also shot on film and has a great score plus much more memorable characters like Qui-Gon Jinn and Watto. Most of the writing (save for Anakin and Jar Jar) is also tolerable at worst and sometimes turns out pretty good!
TPM has many elements that make it the best of the PT, but it still sucks anyway lol.