Also some of the x264 options don't have working default values so one must specify the preset for video encoding. Here's an example:
ffmpeg.bat -i 00001.MTS -acodec aac -ac 2 -ab 128k -sn -vcodec libx264 -deinterlace -s 1280x720 -vpre ./libx264-hq.ffpreset -crf 23 -threads 2 00001.mkv
To make it work make sure you've copied the libx264-hq.ffpreset file from ffmpeg archive into the folder with your MTS file to be re-encoded.
Also you can adjust the -crf 23 parameter to steer the final size and quality of the resulting MKV file.
Enjoy!