Its kinda crazy, back in 1999, Universal was praised for Spider-Man, and a lot of that had to do with the implementation of 3-D onto the moving ride vehicle--the 3-D was the absolute best part of the ride! Whereas Universal's rides that used animatronics (Jaws, ET, Men in Black) rarely received the same international recognition Spider-Man.
Either way, people are never going to be 100% satisfied. Spider-Man would have just been Indiana Jones had it not utilized 3-D...and yet Kong is now just Kong 360 WITH 3-D. Sure, maybe Universal has gotten a little dependent on the technology, that doesnt diminish its merits. Just like people complain about Universal not having AA-based rides, people complain about the AA-heavy Disney about not having enough fast-paced rides.
At the end of the day, 3-D is a game changer for theme park rides. Sure, Universal uses it a lot, but why shouldnt they? They pioneered a new capability of the technology and became critically-praised for doing so.