I recently returned from US and IOA in July. My family and I stayed off-site near Disney from June 29-July 5. We had the 7-day ticket and easily got on everything with very short waits. If I had to give an order of how to do the attractions here's what they would be:
Universal Studios
1) Jimmy Neutron (the line gets long very quick, by noon it was 45 minutes)
2) Shrek (also line gets VERY long early, 45 minutes by noon)
3) Twister (line was never longer than 15 minutes, however we walked right on)
4) Mummy (moderate waits all day, 5 minutes until about noon, then 25 minutes by 5:00)
5) Disaster (30 minute waits all day, you may have to wait a few times before you even are able to get inside the buliding)
6) Jaws (lines not too long during the day, no longer than 20 minutes, if you do decide to ride at night, do NOT wait until near park closing because we ran into the problem of waiting in a 45 minute line with only two boats running)
7) MIB (go through the single-rider line, you walk right on and you don't have to wait outside)
8) The Simpsons (I am not a fan of the show, but this ride was a lot of fun, we were lucky to only wait in line for about 10 minutes, however the queue is very congested and hot)
9) E.T. (15 minute lines all day)
10) Terminator 3-D (queue is entirely indoors, very cool inside)
Then you have time to visit your favorites again. My advice is just follow the lake around and you will hit everything.
IOA
1) Hulk (line gets long early and usually stays long until dusk)
2) Spider-Man (line gets long early, use single-rider when line is longer than 25 minutes)
3) Dr. Doom's FearFall (unless you have a fear of heights, line is rarely longer than 30 minutes, if longer, use single rider)
4) Dudley-Do-Right's RipSaw Falls (when I was here, the line was 100 minutes!! Use single-rider if line is longer than 30 minutes; note: logs are now equipped with lap bars, which make it VERY difficult for larger people and people with long legs to get in and out)
5) Popeye and Bluto's Bilge-Rat Barges (line was about 25 minutes, you WILL get SOAKED, not just wet!!!)
6) Jurassic Park River Adventure (line no longer than 25 minutes)
7) Dueling Dragons (line only 10 minutes, but it takes 10 minutes just to get to the ride, with no one in line)
If you have young kids then you can ride the CITH (Cat in the Hat) and the Trolley ride.
I know this was long, but I hope this helps!!!