For me it was they tried to do too much. In comparison to A New Hope that had Tatooine, outer space, Death Star and a bit of Yavin which they stayed on target with; The Phantom Menace had Coruscant, Naboo surface, outer space, under water, Tatooine and it jumped between them an awful lot.
Dragging politics into it made a mess of the story. I still don't understand A Phantom Menace.
Characters are all one dimensional as already said. That was poor directing because the actors can act but were told to do it a certain way.
Jar Jars 'comedy' was pure slapstick and annoying in comparison to R2 and 3POs mates bickering. Good friends can have a go at each other in a funny way and I could relate to the R2 and 3PO jibes.
Changing the bad guy every movie was a poor idea. They had a winner with Maul but killed him to be replaced by grandad then killed him to be replaced by a cyborg.
The originals had Vader all the way and you could explore his character. Maul was a wasted opportunity. He could of been expanded on in the 2nd and 3rd installments and killed by Anakin/Vader as a climax.
On a personal note I love the style and design of the spaceships in the originals like the X-Wing. The prequels had nothing that inspired me. Just run of the mill space ships. Possibly exception was the Arc-170 but that was brought in too late and had too little time on screen. Never saw those rear gunners fire even though they were chased by droid fighters.
One other thing that bugged me was the extras were just extras. In the original a few nameless stormtroopers had some good lines, crew members too. It made it feel more real with the likes of Piett, Veers, Wedge etc.
I could go on and on but I'll stop here.