If you get one too big, you run the risk of the puppy being afraid of it. If you get a smaller one, you run the risk of it being too small too soon for the puppy.
The size of the holes is adjustable at least in the larger ones.. don't know about the smaller sizes.
I agree with TooneyDogs. Not having to retrieve it from under the furniture every 5 minutes is a huge plus.
Personally, I'd go with the larger one, but that's just me.