Before getting deep into It, I really find It important to first take a general look at both of these games on their own.
AM2R is a fan-remake of the classic game Metroid 2, mostly created with the help of DrM64 and with the help of other Metroid fans. The game was released as a means to celebrate the anniversary of the franchise at that time, and as such the Game is filled with loads of references and connections to other official titles in the franchise for the player to find
And that's honestly the name of the game for this one: while AM2R does have the usual alternate endings depending on how fast you beat It, the Game does reward the player way more for exploring the whole of SR388 in-depth. Additions such as the log which constantly updates as you keep doing findings around the Planet and new powerups make It so the player constantly gets motivated to look for everything It has to offer. All in a really incredible Sprite-work.
So in short: AM2R is an incredibly-looking pixel game which rewards the player for exploring all It has.
Samus Returns is also a remake of the classic Metroid 2, this one was developed by Mercury Steam (known from some of the last Castlevania titles to be released) and was released a year after AM2R.
The game is done in a 2.5D style, with really impressive 3D graphics and sound design for the 3DS.
The Game has some new additions too but most of them involve with something in specific: the action.
This game really rewards the player for going non-stop and getting rid of everything you see in front of you. Battles have been redone to also be more cinematic, giving the player a sense of excitement and motivations to keep looking for more things to fight.
In short: Samus Returns is a really well looking 2.5D title which does push the player into being fast and effective against any danger presented.