Here's the way I tour IOA. The key to this is to be at the gates around 8:30-8:40, so you're there when they open the gates.
First, head to Hulk.
After Hulk, ride Sipderman.
After Spiderman, hit Dr. Doom.
Now, leave MSHI, and head to Suess Landing.
Ride the 3 Suess rides, CitH, One Fish, Two Fish, and Caro-Suesse-el
Go to Lost Continent and ride Both sides of Dueling Dragons, Fire and Ice.
Ride Flying Unicorn if desired.
Now, the main attractions left are water rides. Either Ride them in order of walking counter-clockwise (JPRA, Dudley, and then Popeye), or if you don't mind extra walking, ride Dudley, then Popeye, then finish with JPRA.)
At this point, you have ridden the major rides and you spend the rest of the day exploring the playgrounds, seeing shows (Sinbad, Poseidon), and reriding your favorites.
A couple things about this schedule. If Caro-Suess-el, isn't high on your priority list, either scratch it off the list altogether, or skip it in the morning and come back later, lines for this are usually nonexistent. If you want to ride everything with a minimum wait, this is an order to do it in, it does require lots of walking in 2-3 hours times, but it also gives you plenty of time to relax and soak in the atmosphere once you've done the major rides once.
