My suggestion of having the whole thing more like the Falklands/Malvinas conflict of the 1980's (with the indigenous Gungan's caught in the middle) makes more sense.
The Trade Federation's regime have their own domestic problems which they are trying to whitewash over by mounting a military campaign to reclaim a former colony from the Naboo.
They surround the planet, bomb their cities from space and hold it to ransom until the leader of the Naboo signs a treaty surrendering sovereignty of the planet back to them, calming the unrest back home.
They destroy the Naboo's communication satellites so they can't call for help from the Republic.
They don't realise that the Queen is back at Coruscant trying to find a diplomatic solution until it's too late (thanks to a bit of Sith manipulation).
Not having enough proof and not willing to wait for a Republican investigation she heads of to liberate her home herself.
The Jedi send two observers/bodyguards to protect her and verify her side of the story.
Her ship is shot down and limps to Tatooine to get the parts they need to continue.
They pick up Anakin along the way and finally end the occupation.
It goes in a straight line like ANH and the obvious opening scene little unarmed Naboo being surrounded by the Trade Federation fleet.
The bullies are surrounding the little kid in the school yard, a simple image like the tiny ship running from the giant Star Destroyer in ANH.