When I look back at PFSRPG there are many elements that exist that I think have not been been considered but should have been. The one that jumps out at me the most is that there is a feeling that has been portrayed (intentionally or not) that the scenarios need to be played in order (i.e. 1-A before 1-B, 1-F before 2-A, etc.).
When I look at organized play, I think the main goal is/should be - how do we get this random group of people (usually at a con or local gaming store, who may or may not know each other, and may or may not have experience with the game, with possibly various numbers of episodes/scenarios completed in the OP) together so that they can play a game together. This cannot be achieved if there are strict forced prerequisites such as "Player A is up to scenario #12, but Player B is up to scenario #14" scenario naming conventions aside. This is why PFSRPG has a tier system so that all players between levels 1 and 2 can play in one table and levels 3 and 4 can play in another.
In PFSRPG, once your character becomes too strong, he is forced into a higher tier. Instead in PFSACG, there is a "replay" system that can be infinitely gamed to continuously replay a character until the character achieves near perfection before moving on to the next tier.
I have also seen in some posts people talking about players who only want to play "key scenarios" or want to make sure they hold back until the "key scenarios" are under their belt. Obviously, these are the ones that reward feats. Even PFSRPG has some "favored scenarios" that reward higher amounts of gold for lower difficulty/risk, but you don't want that level of cherry-picking either. This can also make some scenarios deemed inefficient or unworthy to play.
Another issue to consider is - what happens with future seasons? Will players with a S&S character be able to play in the WoTR season? If yes, the issue is that once season 1 arrives, there will be, in theory, twice as many 1-x (and 2-x etc.) scenarios. Does this mean that players will try to play through both sets of 1-x scenarios before moving on to the 2-x? This also provides opportunity for twice as many feats to be earned. Also a strain will be put on the GM/orgainizers to have available every set. If characters cannot cross seasons, then there is less of an issue, however this could limit Paizo's ability to sell S&S (and other sets) in the future after that AP is no longer the current one. I think I would prefer to see the cross seasons be allowed.