When there is SubRip (.srt) subtitle next to the converted video with the same name as the video, it will automatically embed the subtitle
and if the input video has subtitle embedded in it, check the "Subtitles are embedded in video" checkbox at...
the app is still frequently being developed, last update was 4 days ago
https://github.com/SuperrSonic/WiiMC-SSLC
however you have to compile it yourself, since the stable updates dont come out that often
the up/down 3D video is currently implemented in a way that it first converts the video to left/right and then converts the left right for the 3ds, but for some reason its not running the first ffmpeg command to convert to left right 3d
i am...