I am a huge disney fan and so is my DD3. We've been once to US/IOA and once to disney (I went to Disneyworld/Land 5 times as a child- and wasn't too impressed!!) I love it as an adult. Because I wasn't originally a disney fan, I only wanted to do US/IOA, but now Disney is both her and my favorite.
I'm not too crazy at all with US because I've been and love US in LA and its (IMO) much better than Orlandos. But IOA - is the best theme park I've been to in years (because of the rides). To me that's the only thing disney lacks. Disney definately has a magic about it. And yeah they have rides spread out over all 4 parks, but US/IOA has both parks so close (you simple walk around the "pond" and your in IOA. Disney's focus appears to be on there shows, many characters, exhibits, etc. - rides weren't there main focus (and that's okay, because I love disney for all those reasons). In all 4 parks there might only be 3 good rides at each park.
If your children are Nick fans they'll have a great time in Nick Town, and especially in the Nick Studio. This studio was a big deal to me because I remember watching, as a child, one of what is now Nick's trade mark "slime" show (The original show that used the slime was, "You can't do that on TV"). I just simply loved it, but the rest of US was too familiar to me because I went to US in LA several times. I haven't been to the Shrek ride,but I will this summer.
But IOA, is a whole different story. IOA seems to be geared toward both children (especially teens) and adults. It has roller coasters for days (My husband and I love rides). IOA is like a new Six Flags (St. Louis Six Flags is really nice, but the rides give me a headache). My DH and I rode all day long, without DD, in IOA and not once needed an aspirin (I had several in the fanny pack).
Also if you DS in a Superhero fan (Spiderman, the Hulk, and a few others) they'll have a ball in IOA. I heard they will soon add Wonderwomen to their characters (I grew up a HUGE wonder women fan - I thought and still see Linda Carter as being the prettiest women in the world!!!!)
So to make a long story short if you want themed roller coaster rides, like Suess town, Superheros, Jurassic Park,The Lost Continent (they have a ride called Fire or Ice that is a must ride) go to IOA. If you want Blast off on Jimmy Neutrons Nicktoon Blast, see SpongeBob SquarePants, The Fairly OddParents, Hey Arnold!, and Rugratsin Nick town go to US's Nicktown.
Whichever park your family chooses trust me you'll have a ball!!!!!