MP4: MP4 can play by almost all media players which have better compatibility than MKV in video editing and playback. If you want to convert BDMV to MP4 for uploading to YouTube, you can choose this.
MKV: MKV format is larger than MP4 format generally. It supports FLAC lossless audio while MP4 does not. It also supports more features, multiple audio/subtitle tracks. Therefore, people tend to choose MKV when converting Blu-ray discs.