When doing ukemi, "natural" responses often aren't.
Once you learn a technique well enough to execute it, you learn how to set yourself up to prevent the technique from happening. Going ahead and executing the attack in a way that actually allows the technique feels unnatural at that point. "If I do this, he'll do that and then I'll fall down."
This all starts long before there are openings in the techique being attempted. You can really see this when someone makes this mistake in attacking a nage who is experienced enough to adapt the "real" attack rather than trying to work with the attack that was supposed to happen.
On some level, learning how to execute the attack and follow the process through according to the stated plan is a great tool in learning the dynamics of the techniques. It points out the openings left in any attack and the dynamics in taking uke's balance.
Having said that, jiyu waza can be a lot of fun!