Apples and oranges, really.
Both for thrills, and for recent innovations I think the winner is pretty clearly IOA. I wouldn't really call Big Thunder Mountain or Mine Train "thrilling." Even Space Mountain, while it is thrilling in large part due to the theming, isn't anywhere close to the caliber of coasters you find at IOA.
That being said, Magic Kingdom is playing an entirely different game. It's more family oriented than IOA, so they're unlikely to build an extreme thrill coaster with a 54 inch height limit.
Rides like Spiderman and Forbidden Journey are technically groundbreaking and impressively themed, while many of Magic Kingdom's "groundbreaking" attractions are now several decades old. Disney has shown they are still capable of innovation (see Rise of the Resistance), and they have continued to refresh or replace dated attractions. Even Magic Kingdom is getting some more modern attractions, but it is also home to many of the "classic" Disney rides. From both a technical and thematic perspective Pirates and Haunted Mansion were way ahead of their time, but that was 50 years ago. They both primarily use technology from the 1960s/1970s. The quality and charm of these old rides, and their historical importance for the industry are two of the many reasons that they continue to offer great experiences and are unlikely to be replaced by a new shiny thing. Disney fans would grab their torches and pitch forks if either were removed, and both rides continue to attract big crowds. I can't speak for everyone, but for me a trip to Magic Kingdom is about that classic Disney magic. Don't get me wrong I'm excited for Tron, but I seriously doubt it will even come close to competing with Velocicoaster. Honestly I'm not sure it's supposed to and I think that's ok.
A more comparable pairing might be Universal's Hogsmede/Diagon Alley vs. Disney's Star Wars Galaxy's Edge.