The characters weren't interesting, or even worse, were universally reviled like Jar Jar. The main character (both as a kid and as a teenager) was annoying as hell. The story didn't mesh well with the established Star Wars movies, like that thing with midichlorians that was thankfully played down in subsequent movies. For some reason, Lucas moved The Phantom Menace from "Young Adult" territory (as was the Original Trilogy) to "kid's movie", but halfway and inconsistently, so you get Jar Jar and "yipeee!" but also Trade Federation taxation routes -- what the hell?

To be fair, the visuals were also abused by Lucas. I think there's a legitimate criticism to be made of George Lucas and his "horror of the void": when he didn't have the tech/budget, he had to live with vast empty spaces, and the movies got that "Spaghetti Western" barren look that actually made them better. When CGI became cheaper and easier to use, George Lucas decided to fill every bit of empty screen with some gizmo or cute alien screaming at the screen, and his movies suffered because of this.