Eh, Forbidden Journey is my favorite Harry Potter ride... But after much debate in my head, I would have to say Universal.
I feel as if there is a lot more on that side in terms of the Universal park when it comes to attractions and more diversity. There is something for every age group there. Also, there are better accommodations as some of the rides offer stationary seating for people who may not be able to handle certain things during the ride / show. Also, if you do not want to get wet (more importantly soaked) Universal is best, as about a third of Islands of Adventure rides would be out. In general, I always tend to spend more time on the Universal end when I visit as most of my favorites are on that side.
Also, even if FJ is my favorite Harry Potter related ride, Diagon Alley is breathtaking compared to Hogsmeade in my opinion. I literally was in awe the first time I seen it. There is also a lot of little things you can discover in the park you cannot in the other. Hidden gems you could say. Such as if you go into Borgin and Burkes you can touch the Vanishing Cabinet and not only hear the bird chirping, but feel the bird inside it. Also, there is far more shops to explore (as almost all the shops in Hogsmeade are just for display). Ollivanders is much bigger. Gringotts is great. Honestly, the only downside is you won't be able to ride the Hogwarts Express (since it's for park hoppers only).