I agree that the original Star Wars trilogy was more character-driven and the prequels focused too much on special effects, but the prequels have bigger problems. The main problem revolves around the central character, Anakin Skywalker. It's not just a casting problem. I don't think George Lucas really knew who Anakin was, not the way he knew Luke and Leia and Han Solo, and the other original characters. He didn't know what kind of person could be a hero and yet fall so deeply into darkness. I don't blame him for that. It's not an easy character to imagine, let alone translate to the screen. But without finding that character (and the right actor to play him) nothing else in the story really works. The result is that the story of Anakin's fall is neither convicing nor compelling.
There are several other weaknesses to the prequel trilogy. For example, the love story between Anakin and Padme is forced and unconvincing, so the idea that Anakin turns to evil because he's so desperate to save her just doesn't work for me. As Jason says, there's little chemistry between any of the characters.
Lucas seems to have a tendency in these films to write himself into corners and them come up with absurd ways out. In Episode 2 Anakins confesses mass murder to Padme and she forgives and comforts him with some trite remark about, "It's understandable that you were upset." Oh yeah, that's realistic. Having Padme meet Anakin as a little boy in Episode 1 makes it difficult for them to fall in love convincingly in Episode 2. I wouldn't have introduced Padme until Episode 2, and I would have allowed a real love story to have developed there. I wouldn't not have bothered with that silliness about Jedi being forbidden romantic love. It's an unnecessary complication to the plot which Lucas handles poorly.
I don't like the "Rule of Two" for the Sith. It would have been more interesting if several young Jedi had been seduced by Palpatine and were plotting against the Jedi, then to have had Anakin turn on them and eliminate the competition--his final test to prove that he and he alone is worthy to stand at the new Emperor's side.
The Phantom Menace contributes little to the overall story arc. I think the intent behind introducing us to Anakin as a little boy is to give us some insight into his early life so that we can better understand the man he grew up to be, but there's little connection or resemblance between little boy Anakin and grown-up Anakin. The most interesting part of the story is that we get to see a little of Palpatine's early machinations, but there isn't much there, either. If I could rewrite the story, I'd scrap the whole storyline about the invasion of Naboo and tell a different story about a gifted problem child entering Jedi training. I would have liked to have seen Obi-Wan as a Jedi instructor with several students, and perhaps show some of the tension and rivalry between the Jedi trainees. (For example, Anakin is arrogant because he knows he's the best, but he falls behind the other students because he's undisciplined and impatient. Perhaps we see him sabotage or manipulate the other students; perhaps we see him get violently enraged when he loses a competition.) Obi-Wan is sure that he can get the boy under control, but the other Jedi are worried. The boy's first adventure should be tragic and traumatizing, such that we see the seeds of Darth Vader sewn in the boy.
On the Web site linked below, you can read several early drafts of the Star Wars script, written and revised over a period of several years. Some of the early drafts are very different from the movie that was ulimately made. Lucas had enough sense to recognize that something wasn't working in his earlier drafts, so he kept working on them until he got it right, until he had a movie worth making. I just don't think he put the same amount of time or effort into the prequels.
S T A R K I L L E R - The Jedi Bendu Script Site