1. Anakin should have been older in the Phantom Menace. I don't think quite Luke's age, but at least a teenager and someone close to Portman's age. It would make the council saying he is too old more sensible and make Kenobi a little reckless('so was I if you remember' from Empire) to train him. He even could have left the Jedi for a short time to train him. They would eventually relent and let him back in, but it would set up more tension between Kenobi and the council and show that Kenobi truly believed in Anakin.
2. Rule of Two. Silly. No need. If Yoda and Mace's conversation had paid off in some way so that they were actively pursuing Darth Maul's master, then I would say leave it in. However, they didn't do anything with the line, so it is there just to mess with Empire Strikes Back.
3. The Clone Wars should be completely different. In New Hope, when Kenobi talks about the Clone Wars and Luke reacts, it sounded fascinating. That is what I wanted to see most when I heard they were making the Prequals. As it is now, it is basically galaxy-wide governmental repression. Not interesting.
4. Jedis can't get married. Quite possibly the stupidest concept Lucas came up with. Why can't Jedi get married? Because Lucas couldn't find any other reason for keeping Anakin and Amadala apart. Why do they need to be apart anyways?
5. Anakin should have been completely evil by the end of the end of the second movie. The Anakin-Kenobi duel could have been the beginning of the third movie. Anakin, now in the suit, could have then done the Jedi Purge almost completely himself and there would be no need to introduce General Grevous or any other character. I realize I'm criticizing a movie I haven't seen yet, but I'd rather see Darth Vader in action than on the sidelines while a new character has all the fun of killing all the Jedi.