My problems with the RPGA:
1) When running the cons, they often went to some pretty extreme lengths to shove around any other Non RPGA organization into doing their bidding, by preventing them from getting rooms, space, and in some cases, prize support.
2) RPGA changed their charter to include the ownership of any and all material run under the RPGA banner, meaning that any good writers who may wish to run an RPGA event gave up any rights they had to the module they ran. This, from what I understood, drove the group I used to run games in at Gencon out.
3) Living Campaigns - While a good idea, and I'm involved in 2 non-RPGA living games myself, they are not organized well. Since you can run the modules in private, hard core powergamers can create a fake "Game Day", run their friends through modules kindly, make sure they get all the goodies, and simply sit and power themselves up (I know people who have done this). This defeats the purpose of the games to me, which is to have fun, and develope your own character along side others who are doing the same, not grab as much as I can and go.
4) No real benifits from membership other than having to be a member to run or play their games, which are hit or miss.
5) Tournies not created equal - Their D&D Open event was an individual advancement event, so it did not promote good team play. In one case, in the final round, one of the characters (Players got to decide for themselves) needed to sacrifice himself, and was gone for the rest of the round. This player was garunteed to not win the tourny, even if it was in character, and is a poor way to run a tourny.
6) Clerical errors - I never recieved any magazines when I was a member, but I was listed as a paid member for years after I wasn't untill they made all the memberships free (I still have my plastic RPGA card). My father had canceled his membership, and it took the RPGA 6 years to notice. Meanwhile, when I was a paying member, I never got any of the award points that I was supposed to get as a member.
7) Tiered games - I didn't like that there were games that required you to have a particular ranking in the RPGA. I was snuck into one of the expert ones (As a someone else who had missed the con but had a judges badge), and had a lot of fun RPing, and while I can understand that it was designed for more experience RPers, why not open it up and simply give the higher ranking players first dibs?
I was with NASCRAG when they ran their tourny along side the D&D Open. I had several D&D Open judges tell me and others that the NASCRAG event was a significantly better tourny (Team advancement, roleplay/puzzle sovling oriented, some tongue in cheek humor, fun judges). They ran under the RPGA when the RPGA made a power play and claimed the right to lord over all prize distribution for tournies (Happened maybe 10-12 years ago), and they actualy lost some support because people were refusing to sign up for free memberships. And they reciently left the RPGA when the moved to Indy, because of the RPGA trying to claim rights to their module (Which the sell to help support the production costs of running the module and as a reward to the authors). However, their events are still exactly what Piratecat described that he liked in the old RPGA, but with consistantly good judges (in my oppinion), fair and tested modules, premade characters with notes on what they think of the other characters, and an emphasis on roleplay, and mostly fun.