This article applies to using Plex on your local network and not over the internet. If you try and watch a movie over the internet Plex will likely want to transcode the video. My NAS has a quad core Atom processor and it cannot handle transcoding of any kind.
I have tried Plex on a Synology DS1813+, DS1815+, and DS1817+ NAS it could not handle playing most videos in MKV format. Some played okay, but not others. This was due to the requirement to transcode. Transcoding is very CPU intensive and the faster CPU the better. An Intel Atom CPU in a NAS is simply cannot handle the task.
A few months later, I used Handbrake with their Roku 1080p 30 Surround setting to create MP4 files. The Roku setting includes multiple audio tracks (stereo and 5.1), two-pass encoding (slow, but good quality encoding), and forced subtitles. The resulting videos average four to five gigabytes for the average 1080p movie. The video quality is so close to the MKV that most people may not see the difference. I can play the MP4 versions from Plex on my NAS it makes little to no difference to CPU use.
I will keep copies of my MKV files because I like having the best quality version possible. These will be a master copy of sorts. However, I created a version of each in MP4 format for streaming on Plex. When other formats in development, such as H.265, VP9, or AV1 become more compatible with my devices, I will likely be replacing the MP4 versions. I feel that neither H.265 or VP9 are [yet] suitable for home use at this point because it takes an incredibly long time to transcode using these formats even with very fast computers.
Make sure you encode movies using stereo and multichannel audio (5.1 or 7.1). If you do not care about multichannel audio, be sure to use stereo audio. This is because some devices will use stereo when not using a stereo receiver capable of playing multichannel audio. If you do not have a stereo track Plex may need to transcode the multichannel audio track to stereo if you are not listening via a stereo receiver. My Roku will automatically select the proper audio track depending on whether or not I am using the stereo receiver.