I did both in one day. And got in almost everything I wanted. I started out going to Universal side first and got right on the Mummy ride. No lines at all on that side at the opening hours(except for Shrek) at least there weren't when I was there which was in Jan. And I was there on a Sat.
I did the Mummy twice, Simpsons, MIB and then went over to IOA and did Spiderman, The mini coaster in HP, as well as the Harry Potter main ride twice. Cat in the Hat, The Dr Seuss Trolly, then back over to Universal to see Shrek and Terminator. Oh also I did ET which I actually quite enjoyed! Only things I wanted to do and didn't get the chance to were Jurassic Park which was closed, and the Woody Woodpecker coaster. Because that section of the park wasn't open when we first got there. It didn't open until a bit later in the day. And by the time we got back over there it was getting close to park closing and I wanted to do other things more.
I would recommend doing single rider as much as possible. I rode the Harry Potter attraction twice that way and even then there was a bit of a wait, but it would have been MUCH longer in the regular line. Only thing I regret is that I didn't get to see the little show they have during the queue line. But whenever I make it back I will probably do the reg. line once just to see it.
1 thing I really have to complain about those parks though is that they make you store your belongings in a locker before you can ride the main attractions. Not all of them just the big ones. Like Harry Potter and the Mummy. The first time I did it, I couldn't get the thumb print scanner to recognize, and so a park attendant had to come over and assist me. Which lead to half a dozen questions, to verify that was indeed my belongings in the locker. Which took up precious park time. Then on the next ride, MIB my Mom who also had to store her purse in the locker didn't get back to reclaim it soon enough, because she was browsing in the MIB gift shop they make you exit the ride through. Luckily I did go to get my purse before the 20min time limit is up, so I was able to pay the $3 they charged her to get out her purse. Which she wasn't too happy about. And as she wisely pointed out. The park screwed themselves over. Because they forced you to go through the gift shop after the ride to get you to buy something, but your purse is stored in a locker half a block away at the entrance to the ride, and by the time most people go over there to get their purse/wallet, chances are slim they're gonna come back. She sure didn't.
It's a really cheap way to make buck! I mean if queue lines are usually so long you'll never make it back before the 20min time limit I guess you're basically forced to pay the all day rental fee.