Make sure you get your room key before you go to the park! You should be able to get it even if your room is not ready. However, when I went to RPH, my room was ready when we got there at 8:00 AM.
It mainly depends on weather. If there's a chance of rain in the morning that day, go to Universal Studios first. There's shows and rides thst are indoors whereas at Islands of Adventure most rides are outdoors (like Hulk and Dueling Dragon coasters).
If weather is no issue that day, figure out what you enjoy the best at parks. Shows? Roller coasters? Thrill Rides?
If you are staying onsite, this should not really be any problem. You'll bypass the lines and get to do more, so you can just decide where you want to go and switch parks later that day. And still do a LOT.
Even though lines shouldn't be much of an issue, rides like Spiderman (IOA), Hulk (IOA), MIB (US), Jimmy Neutron (US), and Shrek (US) tend to back up in the regular line. I HAVE seen MIB Express line backed up a little bit (not as bad as regular...but still 20 minutes or so wait. Lines (sometimes including Express) back up near lunch time.
Since Shrek and Jimmy Netron are fairly new, the Express line will be more likely to get backed up (they are both right by each other so rides like Back to the Future have very little wait anymore...even MIB's lines are getting shorter...more rides for me! YAY!). So if you want my advice, go to Universal first and do Shrek and then Jimmy Neutron (regular line for Shrek on June 28 at 9:30...40 minute wait already!). then you can either stay at US or head over to IOA to do a few things.
Still, lines aren't as big of an issue with the room key!
