Independant layer skew.
Have a setting where when you shift one layer left and right or up and down but not shift the layers above or below it would be a nice feature. I can think of many functions where this would be helpful. To give a visual example of what I am talking about take 2 pieces of paper. Lay one above the other stacked perfectly. Now move the top one to the side slightly and keep the botom one stationary.
Useing this you could align something from one layer beter with another layer that might be slightly off from its proper location within the picture.