RetroDECK is just one of the ways you can set up your Steam Deck for emulation and their team recently put up a rather great sounding upgrade in v0.7.0b.
EmuDeck is more complete, and is easier to setup especially for recent console (e.g. Switch). However it's a script that installs a bunch of flatpaks and puts files all over your device.
RetroDeck is a self-contained unique application so it's cleaner, but last time I checked it was a bit more difficult to get Yuzu to work.
Also, EmuDeck creates individual Steam games for each of your game while RetroDeck is a launcher (EmulationStation) for all your retro game. Whether it's a pro for one or the other is up to personal taste.