Fuck this idea that "Attack of the Clones is actually the worse one, Phantom Menace is better then Clones" Attack of the Clones was WAY better paced then this movie.
I'd actually say that Phantom is better paced, and is still better.
Phantom has flaws, as you list above, but I still put it above Clones (and a no. of other SW films). Phantom has an overall solid story structure, as flawed as it may be. It's a classical space adventure with understandable stakes. Yeah, we might be a bit hazy as to exactly why the Trade Federation blockades Naboo, but we understand - bad guys, princess flees, (Jedi) knights help her, find "the special," return, restore the kingdom, etc. In contrast, it's hard to say exaclty what kind of film Clones is.
Is it a mystery? Well, it's not that compelling - the Padme assassination sub-plot gets forgotten about, and the mystery side only accounts for Obi-Wan. Is it a romance? Well, again, that's only Anakin, and the romance is lacklustre. Yes, everyone harps on about about sand, but nothing about it is convincing. I actually like the IDEA of Anakin and Padme, but while I can buy Anakin being attracted to her, not so much the opposite, and there's nothing in the film that sells it. In Empire, Han and Leia admit their feelings while on the run and in grim circumstances. Here, Anakin and Padme fall in love while rollicking in fields, like there ISN'T an assassin after her.
Oh, and Anakin's terrible. Not that Anakin was a paragon of character in the previous film, but a kid being a kid is something I can at least understand. Here, I get what Lucas is trying to do, and in terms of plot, Anakin's arc is set up well (e.g. death of his mother, his inability to deal with loss, etc.), but in execution, he comes off as a pouty brat. Sometimes, the dialogue doesn't even make sense, like, Obi-Wan will chastise Anakin for being impulsive, but it's Obi-Wan who smashes through the window to catch the orb. And this all climaxes in a giant shootout between two armies we barely know. The Separatists are bad because reasons, here comes a bunch of white armoured guys to pew-pew-pew, cue an absolutely terrible lightsaber fight. People have pointed out that the Maul duel in the previous film lacks emotional stakes, and yes, they're correct, but at least the fight itself is paced well. The Dooku stuff is just plain bad. Even regardless about how you feel about Yoda, it's poorly shot, poorly paced, and there's no real emotional depths. Again, contrast this to Empire - everything in the film builds up to Luke and Vader confronting each other, and I mean everything. It's what drives Vader, who drives the Empire to pursue Han and Leia, to set up the trap on Bespin, etc. Here? Dooku's just some guy.
Oh, and Boba Fett's here because...reasons. Fine. Sure. Whatever.
Really, the only thing I kind of like in Clones is the Obi-Wan sections on Kamino. There's at least some intrigue there, and him facing off against Jango has some enjoyment. But apart from that, bleh. There's a reason why Clones ranks near the bottom of my Star Wars list, and the only one lower is the Clone Wars movie.
Or, TL, DR:
Phantom Menace is fun. Attack of the Clones is a mess.
This.