Kids suck. I would have liked to have seen an older Obi-Wan and an older Anakin from the outset of the PT. As much as I swooned over Ewan MacGregor and his padawan crop in my younger years, they could have just given him a beard from the beginning and been done with it (and I still would have swooned). The absolute lower limit on Anakin's age should have been 19. That way, we could have seen Anakin being a loyal friend to Obi-Wan, seen him being a great pilot, seen him being a great warrior, etc.
Anakin needed some flaws besides 'being an inherently unlikable whiny petulant teenager'. He needed a big flaw that would lead to his downfall--something that Obi-Wan either didn't or couldn't help him fix. He needed some smaller flaws, too, to give him more character. Maybe he could have had bad luck with the ladies, or have had Qui-Gon's compulsive gambling habit (placing bets on himself in races, or getting kicked out of space casinos because he used the Force to rig the space roulette wheel and space craps), something, ANYTHING to make him a more balanced protagonist.
I hate what Lucas did to Padme's character. I'd have totally been down with Padme being a Queen Victoria-type who was enthroned as a teenager, and had to struggle for power against corrupt regents under Palpatine's influence. I could have even been down with a love triangle between Obi-Wan, Anakin and Padme, if they went with 'jealousy' as Anakin's big character flaw. And hell, if Anakin is going to cause her death, just go all out and have him Force choke her to death, and make the fact that Luke and Leia survived Padme's death be a sign that the Force is strong with them. But that 'dying of a broken heart' thing is flat out insulting.
Never having Yoda draw a lightsaber would have made the films so much better. For the venerable Yoda, the Master of all Masters to sully his hands with the blood and grit of battle is such a disservice to his character, and to the legacy of Jedi we had built up for us in the OT. It's like hearing a story about the Buddha going on a killing spree, or Ghandi being a genocidal dictator of a military state. It just don't jive. I want a Yoda who spends all day in meditation, spouts a never-ending stream of koans, hits people with his walking stick for no apparent reason and eats all of their protein bars. A Yoda who doesn't HAVE to demonstrate his power every five minutes to earn respect, like Vader did.
...or, like was said before, a Yoda who never appears on screen, heightening the mystery and making his final appearance all the more surprising.
The point about how all the Jedi fighting in one big battle with all their lightsabers is a terrible idea is right on the money. When freaking EVERYONE in the story has these powers and weapons, even people who we've never seen before, have no lines, and are never mentioned by name, it makes those powers and weapons not special anymore. (That's one of my problems with the EU, too, for that matter.)
Boo on a virgin birth happening in the same movie where a scientific explanation is given to the Force. Those two things should never happen together in the same series. The Force has to be mystical, because everything else in the series is science/tech. (The fact that midi-chlorians are a complete throwaway plot device is even worse. The story would not be different in any way if they just replaced every instance of 'midi-chlorians' with 'The Force'.)