I've published several articles on “remuxing” video converters, which make it possible to convert a lot of videos very quickly for consuming on iOS. Generally, with today's most widely used video formats (H.264), this only involves converting the audio (if it's not already AAC) and changing the container.
So far, the two remuxers I've recommended the most were the free Subler and (strictly the beta version of) MP4Tools. They're very fast and astonishingly useful tools.
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Review & tutorial: MKV2M4V MKV remuxer / converter for iDevices (and Apple TV)
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