Too much CGI. Everything looked fake even by PT standards. I mean, literally everything. It feels like watching someone play a PS2 game or something. All the environments are fake, half the characters are fake. Lucas just went way overboard with the CGI in the second two prequels, but ROTS gets the worst of it. Never once am I able to be immersed in the movie. The lava on Mustafar is obviously fake, the space battles are obviously fake, the clone troopers are obviously fake, even things like the Jedi temple are obviously fake. Everything is overly shiny and clean. I just really hate the entire visual aesthetic of the film. At least Attack of the Clones had semi-interesting environments on Kamino and Geonosis.
Bad writing, both characterization and dialogue. This is a constant throughout the trilogy, but some of the most baffling decisions are made here. People hate on Clones’ sand line, but “You are so beautiful - only because I’m so in love - no, no it’s because I’m so in love with you” is not only the worst line in a Star Wars movie, I genuinely believe it is the single worst line of all-time in any movie without exception. Also, in a span of like five minutes Anakin goes from Jedi to conflicted to SLAUGHTERING CHILDREN ULTRA-EVIL. The whole transformation is way too rushed and unbelievable. Knowing Anakin is a serial child murderer also makes it difficult to believe Vader could be redeemed later on and seems completely out of left field, out of character, and unnecessary. Lucas can’t claim that these are children’s movies and then throw in both shit like Jar Jar and mass child murder (by the protagonist no less). Talk about tonal inconsistency. The child birth death is a horrible plot device too. You’re telling me that in this extremely advanced society with amazing technology everywhere, people still die during childbirth? You can make blasters and ships that travel at the speed of light but you can’t think of a c-section? Wat.
Tries too hard to tie everything together, in the process ironically creates more plot holes. Why did they wipe C3PO’s memory but not R2’s? How did Qui-Gon figure out how to become a force ghost, and if only he, Yoda, and Obi-Wan have this knowledge, how did Anakin become one? Why did Luke get stuck on a desert planet living a hard life as a poor farmer while Leia gets to literally be a princess? Why did Yoda and Obi-Wan give up so quickly? Why did they not fight the Emperor together? How were the clones so easily able to dispatch of every other Jedi? It’s like Lucas was just like “oh shit, I’ve wasted two movies without explaining any of the questions a prequel trilogy is supposed to, so let me just throw it all in here at the last minute.” It just doesn’t work and makes a jumbled mess. If Lucas had split the plot of ROTS over all three prequels instead of meandering with pointless stories about child Anakin, trade routes, a terrible love story, and clones, it might actually have been good. Literally the only important information in the prequels is shoved into this one movie.

And keep in mind this is still the best of the prequels. Says a lot about how bad the other two are.