It would be cool if the Naboo pilots held out for a long time slowly being worn down by the sheer number of the droids and then just as it looks like they are all going to die, the Jedi turn up in fighters and the droid control ship is destroyed by Obi-Wan from inside after killing Maul on the ship instead of on the planet.
The Jedi come across as heroes for once at least.
It would explain why the whole council are on the planet at the end of the movie.
That would be hard to pull off, but it could be worth it if they can pull it off.
I have an idea for Darth Sideous thing as well. Like some already suggested, his identity should not have been revealed so early. What if trade federation were getting their orders not from him, but instead from Darth Maul? (like a chain of command, master gives orders to his apprentice and apprentice gives orders to others. Because why would master bother with this sort of thing personally? He is trying to keep his identity secret after all.) Since Darth Maul looks quite intimidating, it would make sense they are afraid of him and when Yoda says “there is always two, a master and an apprentice” there is even more impact and suspense, because other one is not revealed yet. It would work better I think. Also, this way episode 1 could be dedicated to Darth Maul, Episode 2 to Darth Count and so on. (Also, it would make you wonder, who is mysterious character? Is he scheming something big? Than BAM! In episode 3, you get to meet the Emperor, but with more impact.)