You have to understand the point of Plex. The idea behind Plex is to run a server that is as format-agnostic as possible, allowing the widest possibility of clients to utilize it. The problem it is designed to solve is that music, movies, and tv shows come in a variety of formats and resolutions and encoding, and each device you want to watch those things on typically only support a small handful of formats, encodings, and resolutions; thus there is a need for software than can micromanage all those details for you seamlessly. The strength of Plex is in the server, and what it does.
Plex Server allows nearly any type of client to stream from it. Any resolution, any encoding preferences, anything. It does this by transcoding on-the-fly to each specific client's preferred way of receiving video. This allows you to load the best possible quality file onto the server, and not worry about the client device's requirements. Watch on iPhone, the Plex Server transcodes into h.264 video AAC audio and at the iPhone's resolution. Watch on the TV that doesn't support h.264 or AAC, then Plex Server transcodes into something the TV does support. That's the beauty of Plex. It's not merely a media player. And trying to merge the server function and the client function into one device sort of defeats the whole purpose.
If you want merely a native media player on AppleTV, Plex is not the right tool.