I agree, she does seem to be a bit stronger than the others. I think to some extent that the usefulness of the level threes depends on you deck. For a Falkow deck, you're going to want as many copies of the Witch Queen in your playing set as you can because she's a great card that works with many different Falkow strategies in different ways. In later sets, maybe cemetery control will be more important and she herself will be less important in the playing set as well. I would say that Guardian Sphinx is pretty powerful too, especially if you're playing Gowen. Almost no Gowen cards have DF, so the penalty of Guardian Sphinx is not a big deal to a Gowen deck. Harpy and Skeleton Master are probably the weakest LP 3's. Really, losing AGI always sucks, and losing a unit card from your card set in the end game -- when cards are scarce anyway -- can really hurt too. Still, it's possible in certain decks that different ones would be better.
Right now, the only bad side about using the Witch queen as a soul card for non-Falkow is that it makes it more difficult to use the soul skill of LeBeau, which is a great end-game soul skill. In the end game, very often you find yourself with one big unit on the field and not much else. LeBeau's soul skill makes that one big unit super tough... turning him or her into a one man army.
As a follow up, I'd say the number one weakness of all the LP 3 cards is how awesome the Soul Skills of a lot of the LP 1 cards are. As for LP 2 cards... that's another thread.
"Scissors are overpowered. Rock is fine." -Paper