I've voiced my opinions on the Academy before and although I started losing respect for them when Forest Gump won over Shawshank, the final straw was when Sean Astin didn't get a supporting actor nomination for any of the LOTR movies.
I agree with you there, but it's had for me to loose respect when my peers and I don't agree (any peers, not just the academy) when my peers are judging by the same set of criteria. I personally think the Shawshank/Gump year was one of those years where it was a tough choice (so was Pulp Fiction). Was Shawshank a better film? Maybe. Was it crafted any better than Gump? I don't think so. They were both outstanding IMO. But, I still can see why Gump won. As far as Astin, he was outstanding and it was a crying shame that he wasn't nominated, but best supporting actor is always a tough one because usually, everyone nominated was equally outstanding. And I agree with Bill Cable too about Jackson. His was the better performance, but what are you going to do? Academically critiquing a film and or performance can only take you so far. After that, it's about which one resinated more with you, and I can't find fault when you have a group equally outstanding choices and your personal favorate didn't make the cut.

Besides, for as much as the acedemy gets it wrong, the do get it right. Case in point, Crash winning best picture. It was.