My background: I've played in the RPGA for over ten years, stretching across three editions of D&D.
In PFS I see many of the same failures that led to the significant decline in RPGA participation, but perhaps moreso than any other issue, I find the full-page adventure log to be the largest offender. Rather than have four hours to play in a four hour session, we are forced to give up thirty minutes of time to do arbitrary paperwork, wasting hundreds of sheets of paper per convention and cluttering character folders all in the name of "protecting" us from the cheaters.
In my experience with RPGA, I have found that, no matter what precautions the campaign might take, if people want to cheat, they will. No DM is going to demand to check the character logs of every single player that sits down at their table, as not only would it generally be a tremendous waste of play time, but also it would be quite insulting to the players involved. Considering the insignificant portion of the player base that resorts to cheating and also the utter failure of the log sheet system to prevent that insignificant percentage from cheating, I suggest we eliminate the log sheet system entirely.
The second major issue I have is with the way treasure is handled (another holdover from Living Greyhawk I might add). In the current model, if the party finds a particular item, they can't just take that item; instead, they have to sell that item for half its value, then purchase the item with their own coin. This leads to situations, especially at higher levels, where authors can give their NPC's immensely powerful magic items which they don't have to worry about the characters acquiring, because the characters will never be able to afford them. Again, the premise here is "protection" of players from the greed of other players, as well as to prevent characters from becoming overly powerful from acquiring too many magic items. Instead, such a system leads to adventures that become increasingly unfair at higher levels, with enemies carrying entire arsenals of magic equipment and characters who are too poor to afford more than a few low level items and barely enough coin for the material component of the almost guaranteed to be eventually needed raise dead.
Oftentimes I've heard campaign staff reply that, due to the vastness of scope, living campaigns can not be run like standard campaigns. Now, while I somewhat agree with this sentiment, I do not agree with the methods you've chosen to implement. Every player is fully capable of tracking their own gains of treasure and experience; they do not need the PFS staff to hold their hand in this matter. Don't punish the vast majority of honest players by making them jump through hoops that the dishonest players can already easily circumvent. And if you are concerned characters might get too many magic items, tell your authors to stop giving those items willy-nilly to NPC's.
Frankly, to me, it comes down to an issue of trust, and the current system to me illustrates the lack of trust the campaign staff has for its players. The vast majority of us are grown up enough to be civil and fair with our fellow player, without resulting to cheating or bullying others to get a particular magic item. If you'd just let us show you, I think you'll find a much happier and much more devoted player base. And if the miniscule population of players that are dishonest want to cheat, let them. Neither you nor I can stop them, but eventually they will simply wake up one day to find that no one else wants to play with them.
Anyways, that's my two cents, and I hope someone in charge takes my words to heart. At times, the RPGA has provided me with some of the most memorable fun I've had, and I hope eventually PFS can do the same.