Recently tried few video player apps on my new iPad. AV player HD, EC player, Buzz player HD, ACE player and OPlayer HD...all of them have problems playing back 1080p Mkv. The best solution right now, IMO, is to stream the HD videos from the computer to iPad. I have used Air Playit to stream 1080p Mkv to iPad with very good result. The app is free. Give it a try.
PS. I have asked the developers for the video player apps mentioned above about the possibility of adding Quad Core GPU HD video decoding support in the future. Only OPlayer people responded saying they are planning to add this feature in an update soon.