Both parks are essentially circles so you can work your way around according to how much you want to do. You can't count on RRnR being open first thing in the morning (or even at all). If I were doing US I would start with Jimmy Neutron (many times US opens earlier than the posted opening time with only Jimmy Neutron and The Simpsons open) then The Simpsons. As you head to The Simpsons make a note of what time Terminator 3D opens. Do The Simpsons, MIB, Jaws, The Mummy (if it looks like it's going to be crowded you may want to do The Mummy then double back to Jaws), Twister, then head over to IOA.
I've skipped 4 main attractions at US, here's why: Disaster is entertaining but the actual ride part is pretty short and the preshow takes up a lot of time. Shrek and Terminator are shows with plenty of room, you can catch them later in the day when you finish the rides. RnRR is unreliable and takes up a lot of time. If you're determined to ride it I would make it the last ride of the day. That way even if it's a long wait and the park closes they will keep the line open until you ride it.
Anyway, in IOA do Hulk and Spiderman. You'll have to see what the weather is like before you decide on the water rides. If you are skipping them head to Jurassic Park for the river ride, it's a water ride but no the kind that will get you soaked. Then Dueling Dragons. I like the Cat in the Hat ride and the trolley in Dr. Seuss but that's optional.
If you want to eat, Mythos in IOA has won the "best restaurant in a theme park in the world" award so many times nobody else bothers to compete anymore. If you're in US when you get hungry Finnegan's is nice.
After you finish the thrill rides catch the shows you missed at Universal. See Disaster, or The Beetlejuice Revue, or the Horror Makeup Show. This should make for a full, fun day.