It's been a few years - we did my daughter's wish trip in 2001 when she was 3-1/2. If you want to keep your son from being overwhelmed until you can gauge what he's up to I have some advice I can pass along ...
1) GKTW will likely provide you tickets to the four Disney Theme Parks, the two Universal Parks and to Sea World. Also, as other posters have mentioned, some of the characters will come to the Wish Village to meet your son, too!
2) There is a merry-go-round and a ride-on train in the Wish Village itself. Don't be surprised if your son wants to ride these over-and-over again day at breakfast & dinner time. These may build his confidence for other rides at the theme parks.
3) The World Showcase in Epcot is a great place to meet characters - maybe not Mickey, but Winnie the Pooh is often in England, Mulan in Japan, etc. In general I found that Epcot was the least hectic place to do character greetings - it also is the most "open" park so doesn't seem as crowded. It's easy to find Mickey in his "Judge's Tent" in Mickey's Toon Town Fair at the Magic Kingdom. As others have mentioned, find a way to let the cast members know that your son wants to meet Mickey. One of the cast members might escort him in through the "exit" and he'll have a relaxed, private session with Mickey!
4) Sea World is also a great place to go! There are lots of non-threatening experiences - dolphin & seal shows, penguin exhibit, etc. I would strongly recommend a day at Sea World. It is even more relaxed than Epcot's World Showcase.
5) Time your visits to the Disney parks to catch the afternoon parade at each park - nothing too scary or in-your-face at these events, either. It always seemed that the Disney CM's in the parades spotted my daughters Make-A-Wish button and waived, winked or smiled at her!
6) We didn't find much to do at the Universal parks - seemed geared for older boys, not 3-1/2 year-old girls. I understand their rides are more "thrilling" than Disney's so I wouldn't visit their until you know your Son's limits.
Have a wonderful trip - it will truly be a special experience!
