Pete, I have to disagree here. The same people who ran the reffing the past two years are the same people running the reffing now, using the same system. It's one thing to inherit the problem, it's another thing to do absolutely nothing to fix it. I don't know if Dave and Dan just don't have the resources/environment/support to do what they need to do (although I think the existence of Dave *AND* Dan in the dual-weird-role they have now is part of the problem, you just can't have two ultimates) or if Dave and Dan are the problem (they're certainly nice and smart guys, but nice isn't necessarily a good personality trait for ultimate), but I do know that what NPPL is doing now with reffing is the same thing they were doing in 2005 and 2006.
But, that's a bit beside the point. The reffing was not the cause of the problems in the finals. Nobody involved in the reffing made the decision to allow a tie finish. I'm also pretty sure that the decision to overturn the 2nd game's result was Shawn's as well. And it's not just that those individual decisions were bad - by the time Shawn was making those decisions it was already too late. The only right decision for Shawn was to stay in the announcement booth and let the officials make the decision and accept it no matter what that decision is. If Shawn doesn't feel like he can do that, he needs to immediately make whatever changes are necessary so that when San Diego rolls around he will not feel like he needs to be on the field involved in the officiating in any way. The Ultimate can't do his job right if he's not actually the ultimate, and you also do yourself a favor as the league President by isolating yourself from any direct involvement in the officiating. Almost every call is going to have a loser, and it's far better if the losing team is at least mad at the ultimate you hired instead of mad at you personally.
There are definitely some things that Shawn and NPPL have going on where they are kicking everyone's ass. But this set of decisions were definitely mistakes, and it would be a huge mistake to not realize it, accept it, apologize for it, and make changes to prevent a repeat.