Both destinations are great. I usually stay at Disney since I get great discounts there, but since we wanted to see the Harry Potter stuff during our last trip, we stayed at the Hard Rock Hotel for the first few days of the trip, and it was great. Usually, Universal/Islands is a day-trip for me, but after that I totally got the appeal of staying at Universal.
The best perk of staying on-site is being able to use your room key as an Express Pass. We were able to walk onto nearly every ride that way. We were also able to get into the Harry Potter section an hour earlier, and we got to ride the Forbidden Journey ride (which is incredible!) 9 times during our trip.
I'm a thrill-ride junkie, so Universal definitely has more for me there as far as rides. I do miss the Back to the Future ride, though. But The Simpsons ride is pretty fun.
But I had a really great time just on the Universal half of our trip, I'm a much bigger fan of the place now than I was on earlier trips.
That being said, I'm also a Disney junkie, so I love Disney World. There's tons more to do there, and they're much better at customer relations. They have more in the way of shows and entertainment. We were there at Halloween, so we got to go to trick-or-treating at Mickey's Halloween Party at Magic Kingdom, which was awesome. And even though they don't have as many roller coasters, their rides are still pretty terrific.
They definitely need to do something to the Hollywood Studios park, though. It's barely a half-day destination now, and the waits at the Toy Story ride are ridiculous. Basically, if you're not there as soon as the park opens, you're stuck on 90+ lines for the ride for the rest of the day. It's crazy. They need new rides and attractions there - some of it has been there since the park opened.
But I do love both places. On my last trip I was having so much fun at Universal that I almost forgot we were going to Disney World, and then I was having so much fun at Disney World that I almost forgotten that we'd gone to Universal. That's an awesome vacation.