Just mux them into an MP4. You don't need to re-encode (which as pointed about above is time consuming, etc.), you just need to audio and video streams out of the incompatible container.
Grab a copy of the Subler (free,
http://www.macupdate.com/app/mac/31647/subler) and it will de|re-mux a MKV file into an iOS/iTunes friendly MP4. It will also add meta-data (manually and automated), including some nice extended tags that are usually only present in iTunes downloaded media. A 2 hours movie takes < 90 seconds.
Then drop it into iTunes and you can Home Share it to your iOS devices, an Apple TV, easily move it onto an iOS device, etc.