It's funny the things readers react positively to that you thought were on the weak side--that's always a plus. But what I'm looking for is things that don't work, because that's where my attention is needed. I recently got feedback from two readers on something I'm almost done with. Both had one main objection, plot choices that didn't work for them. I immediately knew they were right and fixed those issues. The trick, I think, is to look at a problem as an opportunity, because at that moment your MS becomes stronger--it's the things we don't see that bite us on the ass.
My wife is my best reader. Her calls are almost always right on the money. Not exactly an ideal reader because our tastes differ a bit. Usually, past three times, she's read my book in a day or two, but this is a subject matter that she has no interest in, and she hasn't read this one yet. No amount of reminding, pleading, or showering with love and affection has gotten her off the mark. I am doomed.
But I agree with those who say most "stranger" beta readers are too nice. I understand, and I appreciate that sentiment, but it ain't gonna get the MS in question in shape. Again, I want to know what doesn't work. Opinions though, you know? I think I recall Stephen King saying (at that time) that he had five (not five, six--math!) readers (including his wife) that got his MS before it went anywhere. Six, because author breaks all ties. But if more than half had a problem with a character or a plot choice or what have you, in his mind, they had to be right.
ETA: Just to add to this, it still stings when you'd thought you'd nailed something but a reader tells you otherwise. It can take a day or two to get over the jolt and another day or two to get past your bias-I can get locked into an idea and have no doubt whatsoever that I am right--only to find once the smoke has cleared that I was dead wrong. In the end, we choose.