I have been trying both iFlicks and iVI and finally decided to donate to Subler and MP4Tools.
iVI has nice set of customization features, you can add subtitles, can't precise audio much (they promised to add AC3 640Kbps downstream in next update) and sometimes it feels buggy (e.g. if you enable pass through but have set max 4.5 Mbps, app was supposed to warn you - according to their FAQ - and stick to the settings while it is passing through even 20Mbps tracks with no warnings).
iFlicks on the other hand has almost none customizing features, you can't add tracks, can't add subtitles, can't have influence on the video's high profile (nightlies HB allows this). So it is either all or nothing and after iFlicks you still have to use Subler to add / remove tracks / subs.