In general, a story like the Prequels is very hard to write. A “good guy turns evil” script is not easy to pull off in a believable way, especially in only 3 movies. Yeah, the Godfather pulled it off, but that’s why its revered as a classic. Also, Michael Corleone went from a normal every-man to a very unforgiving mafia boss. Anakin has to go from an honorable, likable hero, to a genocidal fascist cyborg in only 3 films. This kind of story is hard to pull off, and I almost wonder if The Phantom Menace was Lucas’ way of unconsciously procrastinating on all that difficult dramatic writing.
Lucas briefly toyed with the idea of a 12-episode saga. Episode I would’ve been the prelude to the Clone Wars trilogy, with Episode V serving as an interquel between the Clone & Star Wars trilogies. That would’ve given us 4-5 films in which to explore Vader’s rise and fall.
What could’ve been. But this is why I’m partial to rewrites/fanedits which jettison the episode numbers altogether.