I love the A Song of Ice and Fire series, about equally as I do The Lord of the Rings. But I would also agree that you can't really compare the two. They have both created the most complete, "alive" and engaging fantasy worlds that I've ever read but that aside, the two series differ greatly and scratch different itches for me. They are both outstandingly great in their own right though.
Obviously people on these boards will side with The Lord of the Rings, but no reason to trash the other one, please. Besides, that's not really the point of these Tolkienology articles, in my humble opinion.
You are right. The only point, for me, why these could be compared, is to see the difference between the two (even though the latter is inspired by) and recognize what is so great about Tolkien - all that the other thing is not.