Not surprised that there was a 3 hour wait for Harry Potter Forbidden Journey. To do Universal excursion with a ship that is docking in Orlando in the afternoon is really a very rushed few hours.
Even if you buy the fast pass Harry Potter is not included in fast pass.
Forbidden Journey is an awesome ride.
I bet your day was alot better and relaxing then those that ventured to Universal. My wait limit is 30 minutes will not wait more then that for any ride.
The best way to do it is staying onsite at a Universal hotel this way you get the one hour early opening before the rest of the world comes in. Plus even faster if you go on the single rider line if you don't mind sitting apart from your group.