Which brings up more issues. If Naboo had this great space defense system, how come they didn't go up and attack the Trade Federation when they were trying to land (or before)?
They were attacking and landing troops on the other side of the planet, where Naboo's defences were at its weakest due to the sparse population. It must've been a similar strategy that the Empire used on Hoth, but on a larger scale.
1) The movie suggested the Trade Federation landed on the opposite side of the planet (Obi-Wan and Qui-Gon needing to go through the planet core is evidence of this). Why not just park a mile or two outside of the town? I guess the point is there was no need to land that far away.
The Empire had a much more impressive navy and army than the Trade Federation, but the Imperial armada could not fire upon the Rebel's base on Hoth due to a theatre shield. Then one of the Star Destroyers launched a full frontal attack on Rebel ships leaving the base, a huge Rebel cannon fired upon and seriously damaged the Imperial vessel. And these were demoralised Rebels in a makeshift basecamp. Naboo was a long established world, with large cities and modern industries, and a standing military, so their defences must've been denser. And they had a larger fighter contingent that would be effective against the large landing craft, and were also shown slipping through the anti-fighter defences of Trade Fed vessels and outfighting Trade Fed droid fighters.
So the Federation kept their fleet back, to maintain the siege, and landed their troops on the far side of Naboo, avoiding Naboo's main skyward aimed defences.
The droid soldiers are disposable units, but they can't have an infinite number, while the ships and vehicles they go around in are going to be more expensive and harder to replace. If the Trade Federation suffer heavy losses, and have most of their landing craft and a few doughnut warships shot down in a full frontal assault on Theed, their invasion plans would get drastically slown down and the siege could be broken.
The occupation must've lasted a couple of weeks at least, with most of the character's time away taken up on Coruscant.
Also, it begs to reason that if the Naboo people build the power core, they probably have the materials needed to fix it if it breaks. I think the point here was that we never knew what was so vital to the Naboo that this invasion was causing people to die.
Sio Bibble described the fatalities and hardship of the interned Naboo as "catastrophic", Nute Gunray smugly said Bibble's people were starving, we see dozens of Naboo citizens being hearded away by droid soldiers, and a droid officer mentions camps. It was implied, not shown, since
TPM was for family viewing (it was tell not show).