As a seller on ebay, I break up the 2009 US Mint Proof Sets and sell the coins individually.  Thus, I have gotten to know these sets somewhat intimately.  Their quality is appaling.  Following are the details:

Quarter Sets:  The quarters are the only coins that have a good consitent quality.  An occassional coin with a pin scratch turns up, but nothing serious.

Lincoln Sets: Oh DEAR!  These coins often have discoloration, watery looking marks all over, and pin type scratches.  Often the obverse is a bit worse, and there are often these strange translucent blobs on the fields near the edges.  I believe that because these are copper this year, that they seem to be having great difficulty with the metallurgy.  When I get a lot of Lincoln Cents that are discolored or otherwise damaged, I lose money, because these bring 15 dollars a set and up to 6 dollars a piece.  Today I sent back 75 sets to the mint because of cents in particular, though other coins had serious issues.  Return shipping was 159 dollars!!!  I do hope they keep their promise of repaying that cost.

Presidential Dollar Sets: These are usually ok, but sometimes they have issues.  I've seen a few with strange discoloration, and some with pin like scratches and scuff marks.  Alot of these sets have little pieces of dirt and string stuck in the packaging.  This is true of all the holders, but most true of the dollar set.  Also, I see many areas of die chips (which are not damage) that are the same on many coins, which confirms they are die chips.  However, I also find scratches on the dollars, and especially halves that have identical scratches on other coins of the same type.  I don't think they are die clashes, but they must be made in the striking process.

Extras Set:  The Sacagweas are usually decent, though the fields are clear in some and are progressively cloudy in others.  The half dollars, as mentioned are sometime ridled with pin type scratches that may or may not be made in the striking process.  The dimes have been generally good, except in 19 sets in a row where I had 19 dimes with identical edge dings!  Have you ever heard of edge dings in a proof sets?  When looking at the coins from the edge, you can see that there is an indentation inbetween one of the serations of the edge where the dings are.  Is this damage or an error? Either way, it doesn't look good and I don't pass these along to collectors and just take the loss.  The nickels have been sometimes fine, but on some I have very large pin type scratches and thesse semi-circle scuffs that don't look like part of the minting process.  Sometimes the coins are off center by 90 degrees or so in the sets.

Obviously the mint has more coins in the proof set and for circulation then ever in the history of federal US coinage (correct me if I'm wrong on this point).  I have to guess that amount of output is having a negative impact on these sets quality.  In an era when graphic designers recut our coins in lower relief, and the aesthetic impact of much of coinage is lost, it adds salt to injury to have these further issues.  Color me not impressed.