Well, in the movie the Indominous was about as big as a t-rex, could blend into the environment/become invisible, could communicate with raptors to attack the hunting party, and most importantly it thought out an escape.
The Indoraptor was shown to be clearly intelligent in that it played possum when Captain Stottlemeyer (Ted Levine, I just know the actor from Monk) tranqed it. However, the creature was trained to attack anything that the sonar gun shot at and did not question whatever the target was. It didn't seem to really have any goals other than "eat people" and attack what the sonar gun tells it to, which is unlike the Indominus. It was also much smaller than the Indominus. The only thing I can think of that the Indoraptor has over the Indominus is that it could be a bit faster and more maneuverable.
I'd have to go with the Indominus on this one.
SPOILERS:
P.S. I absolutely hated the plot of the last movie, it made no sense! I also really hate the ending with the little girl letting bloodthirsty deadly animals onto the world, why would anyone in their right mind do that? Saving the dinosaurs was a stupid idea and the whole clone side plot made no sense. But as a fun monster adventure movie it was ok.