Actually, I recall a fan story about having the reason for invading Naboo is really because they are keepers of cloning technology, and the story was written based of the speculation based on the trailers only and before Episode 1 came out. (You wonder why the Queen and her handmaidens look alike right?).

Therefore the Trade Federations blockade/invasion is correlated to the Sith to get the cloning tech... thus setting up Episode 2 with the Clone Wars erupting... The purpose of the Clone Wars in general is a means for the Sith to destroy the Jedi. We all know this, but it's not blatantly obvious as it should be. Episode 1 should of focused on defining the perimeters of the Jedi Orders destruction by the Sith and that way we understand Episode 2 and 3 as the Sith's master plan coming to fruition.

Considering it was a fan story I didn't use my special photographic memory ability to remember exact details but I did think that as a driver for invasion made sense... Maybe we can salvage that driver and use it as clear means that makes sense to Revisit Episode 1 cos really, ANYTHING is an improvement on that thing and having a clear point would be refreshing...

Also we can use existing cloning facility footage/images from Episode 2 but on a smaller scale in order to drive that plot further. I think before anything, the main driver for the plot should be clear and defined and all the other fixes would fall into place afterwards... The cloning idea is the driver for ALL the rest of the movies and should of been introduced in Episode 1. It makes the ultimate betrayal in Episode 3 make that much more sense.