They had a choice between speed and interactivity. They (wisely) chose interactivity.
Also hard to put the blame solely on UC here when Nintendo was involved heavily every step of the way.
Nintendo and Universal wanted to build a big, interactive, family dark ride, and that's what they did, and from the looks of things they knocked it out of the park. The "problem" is it wasn't the interactive, track switching, racing simulator, dark ride coaster people built up in their own head for 5 years that never would have worked in reality.