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mkvmerge was used instead of FFMPEG purely by design choice (I was more familiar with it and because the job was only to make mkv files), but I should be able to make a wrapper for FFMPEG for those who prefer to use it. Another native solution to make MKV files is also currently being developed, for those who don't have (or want to install) either softwares.
As for other outputs, many don't support multiple audio files or ASS softsubs, or not as much as mkv files are able to. Some people might want to burn the subtitles, or only have one audio track, and enabling those formats depending on the use case adds some complexity to the program. But I think it should be possible to use FFMPEG with the merged mkv as the input to make a MP4 file with one audio and the subtitles burned in.
FFMPEG may enable other formats support, but the more flexible of them remains mkv in my opinion. MP4 could be another supported format (as more widely supported I believe), but the problematic here is the support of ASS subtitles files (I could be wrong there but the only possibility is to burn them in the video, and I don't want to re-encode it). If I add a wrapper for FFMPEG, it might be possible to output a MP4 file. However for the other formats I would need some examples and see if it's relevant to support.
FFMPEG support will be added in v0.4.0, but the support for other file types might come a bit later (as it requires some modifications in the way the CLI works). Since the CLI will be heavily modified for the next version, it should be implemented there.
It would be great if support various output types like mp4, flv,...
and why don't use ffmpeg instead of mkvmerge ?
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