All I can tell is is our experiences when DD (now 6) was around those ages. DD wasn't scared of much at those ages, although she still goes back and forth on thrill rides (i.e. hates Big Thunder, but has always loved Soarin and Star Tours)
Wishes- I think Wishes is your must do. There is something special about watching the fireworks over the castle. One thing you might think about is whether your kids have ever been that close to fireworks. DD loves Wishes now, but when she was 2 and 3, although she loved 4th of July fireworks, we found that the noise of Wishes really scared her to the point we had to take her into a store and miss most of the show. Being inside the park, the fireworks can be a whole lot louder than what you are used to at home. Just be aware that could be an issue.
Fantasmic-- Might be a bit scary or intense for the 3 year old. DD was 2 years 10 months old when she first saw it. It is the first time I have ever seen her scared of any show etc. The villian part went on too long for her at that age (this is the kid who from age 2 would ride the Snow White ride over and over and cried when they closed it last year). We actually felt kind of bad for taking her as she was burying her head in our shoulders and was really scared. I had seen it before, and I had rewatched it on you tube and felt she would be fine with it, but I didn't take into account how loud and intense it can be live, especially if you are closer up. The shooting in the Pochahontas section is particularly loud, as are some of the fireworks. I think it was the loud noise that bothered her when coupled with the villians. It is a great show, but I would recommend sitting closer to the back with littles to make a hasty exit if they get scared and to keep it not quite as intense. We haven't been to the WDW show since then, but we have seen the DL version (which is better), three times and she loves it (it has a Peter Pan section instead of the loud gunshot Pochahontas section though, so that may be a big reason). Fantasmic can involve a lot of standing in crowds waiting too, so that may be something you want to consider.
Illuminations--- this would be our skip it. The problem with Illuminations for the little kids, is that you have to be really close up for them to be able to see as most of it is lower on the water instead of high up in the air. If you are not right on the rail close to the water, someone will stand in front of you and then all the kids can see is the back of the person in front of them and a few sparks here and there. If you are right up at the rail, it can be too intense for the little kids. DD hated, and still hates, watching illuminations from the point where she can actually see it because it is just too close and loud for her. We've tried it a couple of times and she has never lasted the whole show. Epcot has also seemed the hardest to get out of after the show to us, in terms of catching Disney transporation. Illuminations is exactly at closing time so everyone immediately heads out of the park, where Wishes often is at least an hour before closing time and Fantasmic often has at least a first showing a while before closing, so it doesn't seem like the whole park is headed the same way at the exact same time. Sure, there are a ton of people that head out right after Wishes or Fantasmic, but we usually let that crowd thin out a bit and still get out of the park right before the closing crowd. Epcot you can't do that. Every time we have watched Illuminations until the end it has been a madhouse. We usually find ourselves skipping Illuminations and catching the monorail either right as Illuminations starts or we are definitely already heading that way before the show ends to beat the crowd.
