A good website to visit that will give you good info on Disney World is www.allearsnet.com. I think they also have a section that talks about non disney stuff such as Universal. As far as tickets go you can try www.mapleleaftickets.com. As you get closer to your trip I would also check www.mouseplanet.com, they usually give some good info about rides/shows will be closed for rehab etc. I would also find out which day each park is having early entry. Since you aren't staying on property you won't be able to take advantage of that but you will know which park to not go to. If MK is having early entry than you should go to one of the other parks. It won't be as crowded since everyone else will be at the early entry park.
As for a must see, your son will probably really enjoy the Pooh Bear Playground and Toon Town at the Magic Kingdom. At Animal Kingdom they have a playground with sand near the dinosaur ride and at MGM they have the Honey I Shrunk the Kids Playground.
The only other thing I can think of right now (I love Disney, so I can always come up with something) is that your son will be older this time around. Being older he is more aware of things than he was at 9 months and therefore might not be as open to the characters. We went with my neice who at the time was 20 months and she wasn't all smiles when it came to the characters. We still got some great pictures as she was very serious with them and more into studying them and really looking at them. As for the rides, she didn't seem to really care at all. She did notice however that most the rides that she could do were in the dark (Pirates, Small World, etc) and she would only sit with her mom. She wasn't scared of them but she definitely wasn't sure about them. Enjoy your trip!!