PlexConnect is just a way to access the plex library right on the apple TV. It works okay I guess. Apple TV doesn't have an app store, so getting to the plex application isn't going to happen. Plexconnect is a way to point a currently existing app (like Trailers) to the plex server in your home.
Plex has a few features. Metadata, multiple formats, some channels that work etc. All of my content is mp4 so most of it doesn't matter. I also use Subler for metadata and artwork. I personally use plex because it makes it easy to access my plex library remotely. I can pull up the plex app on my iOS devices or a browser from any laptop and view my plex content
Actually plex connect hasn't received much support from plex recently. Im pretty sure the idea was abandoned (but still works).
I was using plex connect with my apple TV but found it to be inconsistent, generate issues frequently and sometimes not show up at all.
Im currently using an iPad with the plex app installed to view content. I simply pick a movie and airplay it to the apple tv from the iPad. It works well actually and I prefer it to the plex connect experience
The best "from the couch" remote control experience with plex isn't going to come from an apple TV. If you want plex content without using an iOS device or plexconnect, you'll need to buy a Roku or Amazon TV that can have the plex app natively installed
The 2015 expected apple TV will hopefully get an app store and a native plex application. We shall see.
Either way, Plex will give you a better experience than iTunes alone when viewing content from your couch