It's not the same thing at all. By the time it was demolished, Dueling Dragons had lost it's main gimmick and had much of it's theming ripped out to awkwardly retrofit it to a Harry Potter Theme. Additionally, the ride itself, while very thrilling and fun, wasn't perfectly unique and irreplaceable. Travel an hour to Tampa and you can ride Kumba, which, sans dueling, is essentially the same experience (heck, Kumba's track layout is probably a bit better). It was replaced by a one-of-a-kind unique attraction in which Universal gave it its all.
MIB:AA, on the other hand, is, in my opinion, the best shooter ride in Florida. Compare its quick-spinning vehicles, huge, elaborate sets and copious amounts of well-designed animatronics to its competition. Toy Story Mania is all screens, and Buzz Lightyear Space Ranger Spin mostly relies on a cheap black-lit "cardboard cut-out" look.
Additionally, as the only shooter ride in all of USO and one of the few attractions at USF that doesn't rely on screens, it serves a very unique niche and plays a crucial role in diversifying the attraction line-up, as well as offering very high reridablity.