Yes, .MKV is a non-standard format, so itunes will never use metadata correctly from it. I would suggest moving away from .mvk if you are looking at long-term compatibility. .MP4 in theory can replicate most of the cool features of .mkv (embedded artwork, descriptions, multiple audio, selectable subtitles), but as of now, how apple is going to choose to implement these features seems very much up in the air (can someone explain how subtitles are currently handled in quicktime?) and they have a history of using non-compliant implementations.
.MOV is apparently 90% the same as .MP4 standards-wise, as .mp4 is based on .mov, but again, it's not an ISO standard and I would stay away from anything non-standard if you want to be able to watch movies in the future.