I don't think this is a complete answer...but the elliptical is better for your joints, especially the knees. I get knee pain with the stepper, but am fine on the eliptical. I'm sure there is more that that, but that's why I prefer the elliptical :-).
I think it's similar to the difference between an elliptical and a treadmill. On the elliptical, you build up momentum: you'll notice that when you stop trying, your legs still do a few spins around. Also, on both the stairstepper and the treadmill, you have to pick your own feet up, whereas on the elliptical, the weight of your other foot does it for you.
Its definitely the momentum on an elliptical that makes the exercise easier. Many people enjoy the elliptical because its more fun or they have knee problems but I say stick with the treadmill or stair stepper (my personal fav is the perpetual staircase) to get more bang for your buck in your workout.
I am going to guess you don't use a high resistance on the elliptical and that is why it is easier. I use a high resistance and there is NO momentum. Which is why I find the stair stepper easier.
Stair stepper vs. Elliptical
