I did have a suggestion in the other prequel thread, with regards a new power source having been found on Naboo. I agree that the current plot really does not make much sense as for a organisation as rich and powerful as the Trade Federation to seize a backwater planet. SO I'd suggest a new power source discovery as a solution... One that would allow much bigger capital ships stations and powerful weapons to be built. Which would explain both Sidious and the Trade Federations interest. You could just include that information in the opening crawl...
i.e...
Following the discovery and harnessing of a new and very powerful fuel cell on Naboo, various factions are vying for control of the previously unimportant Republic planet. The evil and nefarious Trade Federation have been the first to arrive at Naboo and have established a Blockade around the planet stopping anyone from entering or leaving Naboo.
Meanwhile the Trade Federation had simultaneously managed to mire the Republic Senate on Coruscant in bureaucracy, because of this the Republic is unable to send any representatives or military presence to assist the beleaguered planet.
Concerned with the unfolding events, the Supreme Chancellor has contacted the Jedi Order, who in turn have dispatched to Jedi Knights to investigate and negotiate an end to the Blockade...
Just my 2 cents :)