Thank you for your time, I do have time for remuxing (and rushplayer team even wrote a program to do it on ipad, haven't tried it though)
Unfortunately, it isn't very good. (Have thoroughly tested it.) In order to avoid linking to my blog (=self-promotion), let me copy the entire section from my original article elaborating on the converter:
Mkv2mp4
I've also thoroughly tested Mkv2mp4 from the same developer as that of RushPlayer. Unfortunately, I in no way can recommend it. It could only remux only one (h264_720p_mp_3.1_3mbps_aac_shrinkage.mkv) of the numerous test MKV videos (I use all the standardized test MKV videos accessible HERE): one that already had AAC audio (and no subtitles). The other test videos resulted in the following:
264_1080p_hp_4.1_40mbps_birds.mkv (no audio!): progress indicator quickly flashes but the app doesn't, then, convert
vc1_1080p_ap_l3_18mbps_ac3_hddvd.mkv: nothing happens
h264_1080p_hp_4.1_10mbps_dts_unstyled_subs_monsters.mkv : stays at 0%
h264_720p_hp_5.1_3mbps_vorbis_styled_and_unstyled_subs_suzumiya.mkv : stays at 0%
xvid_480p_as_l5_1mbps_he-aac_foreign_subs_matrix.mkv: nothing happens
h264_720p_hp_3.1_600kbps_aac_mp3_dual_audio_harry_potter: -. The first audio track is converted to static noise; the second results in a crash at either transcoding or playing time. (The resulting file of the second is useless)
h264_720p_hp_5.1_6mbps_ac3_unstyled_subs_planet.mkv: stays at 0%
Note that almost every of them could be reliably converted (along with subtitle migration) with the desktop-side conversion tools.
All in all, stay away from Mkv2mp4, at least for the time being. It's just plain incompatible with a lot of audio / subtitle formats, unlike the desktop (de)muxer tools (avidemux for MKV -> MP4 conversion and audio recoding; iMkvExtract + Subler (+ Jubler) for subtitle migration).