Alex focused on mechanics with some nice analogy:
Sometimes it's a matter of taking an event or a scene and moving it sooner, or later, or trimming it out. Move a single scene, and everything may fall into place.
All of these notes are really about the mechanics of the story: how the engine of the story works. It's the difference between a driver saying that the car tends to fishtail, and the engineer saying the center of mass of the car is too far forward.
These are the kinds of notes I most like to get because they make the fix easier. If you think the problem is that the car fishtails, your "reader" response is to drive the car more slowly around corners. Your "writer" response is to move the center of mass, or to throw on a spoiler to push the rear of the car down onto the road. Then your story corners nicely at high speed.
And Lisa pointed out that it's smart to determine the objective of the notes:
When someone asks you for feedback on a script, first ask what kind of feedback they want. Is this a very rough, early draft, and they’re still working on the structure? Or is is nearly finished, and they’re doing a last polish? This should guide, but not limit your note-giving.
If someone asks for small, final draft notes and you spot a huge plot hole, by all means, bring it up. But if they’re still working out story issues, don’t sweat the dialogue - it will probably change as the story does.
In many ways, they're both talking about 'targeting' your notes at specific problem areas. But once the story's working and the structure's sound, there's a new target to focus on...where you want to sell it.
I was recently story editing yet another Canadian feature...a good script with a nifty hook, but a mixed genre picture (e.g. like an action/comedy, or a historical/horror). We were down to the small points of the deal, as it were, in terms of character/story/structure/dialogue/ pacing/logic notes, but with a little nudge in one direction or another, this particular screenplay could be sold to either a Lionsgate or Maple Pictures, or to the CBC. Two very different animals to say the least. It seemed the script was trying to be appropriate for both, and thus ended up not quite right for either.
So my last big note was for the writer to pick a target destination - be it company, studio, or network. Decide where he wanted to sell it, and then hone every detail to appeal specifically to that particular entity.
Trying to be everything to everybody when taking it to the marketplace can spell a quick death for a promising screenplay.