Honestly, I don't think the Academy necessarily has it in for anyone. I think it's still the overwhelming mindset that drama's should win.
If there is any kind of open bias, I think it's a bias against movies not made in Hollywood. In that case, there's definitely reason to wonder if people do have it in for LOTR and Star Wars. Both saga's were made far away from Hollywood. LOTR got made entirely in New Zealand, which is like 10,000 miles from LA, and Lucas has always eschewed working in LA, preferring to work out of Marin County, London, and now Australia.
THAT could be a serious consideration as to why these movies get snubbed. A lot of the Academy is based out of LA, and they want to keep the movie business in LA, along with the jobs. Get that mindset going with a lot of the voting members, and it can have a big impact.