Mainly due to anamorphic encoding compatibility issue, Plex trasncode files for sync that are perfectly playable on the destination device (eg Ipad, Android Tablet, etc).
The result is a compatible file, of course, but this taxes the PMS CPU, and forces the user to wait for the trasncoding to be ended before syncing, which is often unpractical.
In my case almost all files are directplayable by almost anything, but my little girls still can't sync files to the ipad's without waiting for full transcode, when instead the files stream in direct play if online...
Please, create a set of option, possibly in the sync panel of the activity tab on server, where the server manager can choose to "direct sync" files that would "direct play" or even maybe "direct stream" by just remuxing them without reencoding.