I think that in all of the jujutsu-based arts, including judo, many techniques are more appropriate for certain body types than for others. Of course, the technique has to be appropriate to the situation, too.
It's always harder to do a full throw (hip, shoulder, neck) on a person who is shorter than you, because as you've figured out, you have to get below his center of gravity to get him to go over. That means you really have to crouch by bending your knees. If the person is heavy, too, that makes it even more difficult. If you're older and have aching knees, like me, these are usually suboptimal techniques.
The sweeps, reaps, trips and drops (think any technique with the word "otoshi" in its name) tend to be easier for taller people. In the clip that gambatte posted, you can see how easy it is for the taller guy to unbalance his opponent backward and to the corner.
Sometimes against a shorter opponent, you can drop to one knee to throw. In addition to getting you below their center of gravity, it actually accelerates the throw - to their detriment.
When teaching in a self-defense context, I usually advise taller people to think of other techniques besides hip and shoulder throws when they're up against a shorter, heavier opponent. It just makes sense - try to use a technique that is best suited for the particular situation.
