Metroid 2's issue was just that it was on Gameboy, which is only an issue when you factor in Super Metroid coming out IMO. It was still better than original Metroid (which IMO is complete ass even for an NES game)
AM2R was just like really fucking good.
The original NES Metroid is indeed pretty ass, the lack of a map ruins it, I was pretty disappointed when I tried it.
The Sonic Cycle?
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As for games this happened to. I've not seen Silent Hill mentioned. Silent Hill 4 was a huge turd when it released, but since then western devs and Konami turned the franchise into a cynical cash cow that completely misses the point. Now Silent Hill fans pretend 4 was an underappreciated classic, unironically praising things like unkillable enemies that damage you just by being in the same room as you, and a plot twist where a man thinks an apartment is his mother, because at least it's not SH Downcoming, HD Collection, or pachinko.
One that people generally agree on, Starfox Assault. I liked it at release, but it was hated by the fanbase because it was short, and on foot missions were a betrayal. Since then, the series have devolved so much (Command, Zero) that Assault is viewed as almost the last great Starfox game.
I never hated Silent Hill 4, it was always a pretty solid but flawed game, but it's really too bad that it now seems even better retroactively since it was the last "real" Silent Hill game.
What chaps my ass about SH4 is there's zero reason it had to come out only about a year after 3, it should have come out in 2005, giving the devs plenty of time to polish and improve the game and not have to reuse the same levels twice, so I totally blame Konami for the game's flaws and not Team Silent itself, they did the best they could given the timeframe I'm sure Konami gave them.
Hmm, okay, let me throw three to the ringer since everyone is doing and lets see if you guys agree/disagree
Bioshock 2
Arkham Origins
Bioshock 2 had its flaws, sure, but it was still a touching story with gameplay that surpasses the original's in my opinion. I still love 1 more but I think that calling 2 unworthy is just extremely unfair. Ironically or fittingly, depending on how you look at it, I find Bioshock Infinite preeeetty fucking overrated, the two gun slot shit really annoys me and the whole quantum physics oozes of the "intellectual" crowd that THINKS they know what they are talking about but they are as clueless as you as they hope you assume they know what they are talking about. You are free to disagree, of course.
Arkham Origins was more of City, sure, but Im a huge fan of the Arkham series so I never minded that much. Do I prefer Origins over City? No but I still consider it major part of the series thats worth playing. Feels good playing as a younger, inexperienced and quick to anger Batman. I guess I just dig these type of stories. My only issue was throwing Black Mask under the bus for more Joker when I really think he should have been a sidequest villain at most instead of a major one. Bane was done amazingly in Origins tho, no doubt his best in the series.
The trouble with Bioshock 2 is the story just doesn't give you much to chew on, as a game it's good but there's nothing even coming close to the first game's big twist, which is one of the main reasons why the first game became so legendary (no twist has ever freaked me out as much as that one, game or otherwise)
Bioshock Infinite is indeed very flawed, the big trouble with Infinite is that it's not at all an "immersive sim" ala System Shock, Deus Ex and the original Bioshock, it's just a typical FPS with a few "immersive sim" flavoring thrown in and nothing more.
Story wise though while the sci fi stuff in Infinite doesn't make a lot of sense, it's kind of chilling looking back on today with it's theme of an America stand in destroyed by a Marxist revolution happening thanks to racial tension, given all the shit that's happened since the game came out it seems very much like a Metal Gear Solid 2 situation (though not as much)
Bioshock 2's story has aged a little well to since it's also about a collectivist revolution being led by a lady with cat eye glasses, what does that make you think of? Basically real life turned into a Bioshock game these last several years lol.
Arkham Origins is a perfectly solid game I had a very good time with being a big fan of the Arkham series as well, yes the reused areas of the map are kind of lame but people overreacted way too much to that, it was still absolutely worth playing and I'm glad Arkham Knight had a homage to it establishing it as definitely canon.
And yes, Bane was very cool in Origins, there's some fun trivia for me as to who voiced Bane in that game, the actor also voiced a character in one of my favorite animes.