I think it'd be great if you can rotate/scale pattern for Pattern Stamp Tool before applying it. And if you could rotate and have an 'aligned' option for texture settings of the Brush.
Turning 'Aligned' off is great thing when you want your pattern to be slightly more random and I can't understand why Texture setting of the Brush doesn't have the the same option. On the other hand, Texture has scale option which Pattern Stamp doesn't have. Which is odd as well.
For example, on the left side is default behavior of the textured brush: no matter how many strokes you do, you'll always get holes/spots in the same place. And on the right side is how the same strokes'd behave with 'aligned' option turned off: