I had heard it didn't actually do very well. But I must've been wrong, since Nintendo let Mercury Steam do another one.
Taking it as a standalone game, I think the map design is absolutely terrible, with each area being a sprawling mess with no rhyme or reason to why things are where they are, aside from things that are clearly there to ensure you have to come back later when you collect a new powerup on the other side of the planet. There shouldn't be two rooms of lava in the middle of a sandstone temple, it makes no friggin' SENSE.
The melee counter mechanic wound up making getting around a chore since they made everything hyper-aggressive to create chances to counterattack, so you just wind up waiting for the inevitable attack so you can counter, since just running past isn't an option.
I'm also still mad about the random firebug trap costing me a half-hour of gameplay to a unique mechanic that is absolutely not obvious.
I have heard that Mercury Steam toned down the melee counter stuff significantly. I hope they have more thoughtful map design now, too. I've seen things I genuinely like about Dread. And as it isn't a remake of a game I hold dear, I'm less likely to get mad over story and presentation decisions.
Not really a problem with the game as a game, but It was EXTREMELY obvious that they didn't want to include the spider ball by the way they immediately started slathering slime all over the walls to make sure you stayed on the right path. I wasn't actually SURPRISED by that, but I WAS disappointed that they kept it in while removing the singular thing that made it fun.
As a Metroid II remake, well... Wall of text as I nerd out here. Top-level summary, it is less a remake of Metroid II and more a caricature of Metroid II.
As I see it, there's three main story arcs going through the game, and Samus Returns misses all three of them. (In fairness, AM2R fumbled some as well. It was not the Metroid 2 Remake I wanted to see completed, though I respect DoctorM64 for seeing it through when everyone else gave up or just moved on, particularly as he actually had to learn how to program to make his game.)
1: There's a repeated theme in the text associated with all the games in the series that just a few metroids could wipe out all life on a planet. Metroid II is the only game to SHOW this, with non-metroid life becoming rarer and more durable the deeper into the game you get, and the final two areas featuring ONLY metroid life.
Samus Returns drops all the enemies all over everything. Every non-metroid enemy in the game is scattered over every area OF the game. Thanks you YouTube, I know that even the hatching grounds around the queen's lair are teeming with life. (Incidentally, AM2R fumbles this subplot in a different and more subtle way, by including numerous non-metroid bosses that are actually far deadlier than the metroids themselves.)
2: The first metroid you encounter is just lounging around wherever. I mean, why wouldn't it? The 1200-pound grizzly bear sleeps wherever it wants, because nothing will mess with it. Through the course of the game, the metroids start nesting in more secluded and harder to access places. Little twisty tunnels in far corners, off behind hazardous terrain, and late-game in caves hundreds of feet up sheer cliff faces. To be blunt, they start nesting like prey. One of the two omegas is unique in that he spawns pressed against the far wall of his room and facing away from Samus, implying he was running away and fights because he was cornered. Samus' genocidal rampage has taught the metroids fear. It is a Terminator game where you play the killer robot.
There's none of that in Samus Returns, just mazey pipes everywhere because Metroid is a game of mazey pipes.
3. SPEAKING ABOUT GENOCIDE... the manual makes no bones about the fact that Samus has taken on the task of rendering extinct a species that ain't doin' nothin' to no one, and couldn't leave the planet even if they wanted, to because someone else might decide to try and use them as weapons. The game is, to my eye, structured to make you uncomfortable with this. "Pipe enemies" don't spawn infinitely, as Samus burns out their nests(except for the one nest that the Gamma burns out before you get to it). Metroids hide from Samus, one even fleeing in terror. The keening wail of the queen metroid after you kill the last of the larvae. Hell, even the title screen soundtrack is destroyed by missile explosions and low health buzzers. Maybe the metroids DO need to die, but it is a somber undertaking, not a task one should find joy in.
And in the end, Samus refuses to finish the job. She shows mercy on the last metroid. There's a redemption arc for our killer-for-hire. While Samus Returns attempts to sell that show of mercy, it is not thematically appropriate for the game Mercury Steam created. Their game is, in its entirety, a celebration of violence rather than a condemnation thereof. The little mini-cutscenes when you melee a metroid make me uncomfortable, but it is with the thought that someone could start off with Return of Samus and end up with "cutscenes of Samus pinning a metroid to the ground and cramming her gun into its mouth would be cool, and by cool I mean totally sweet".