Seriously why? 

Here are the sales of Metroid according to this site: 

Is it because it's a single player shooter game so sales should be limited?

Maybe. Let's compare Metroid sales to another shooter series known for its single player!

And it turns out the highest saling Bioshock game is 2.5 million just like Metroid Prime! Except these game are multiplatform so you have to add all the systems together to get a better picture. And when you do that, this series has already have mutliple software that out sell Metroid's top selling game.

Okay, so the genre isn't a big deal... Maybe it's because the game has such a passive story, a lot of backtracking, and isn't entirely easy to get into for new players. 

Wait that sounds like a popular series called....

Actually this series has sales quite similar to Metroid! But again we need to count the multiplatform sales to get the whole story. And Dark Souls III which only has 1.8 million sales total just released this year. It won't be too surprising to see it match the first Dark Souls 3 million sales. Something a single Metroid title has never accomplished in 30 years. This is quite disheartening for a series with games that defined a genre and rank consistently high in the greatest games of all time lists.

However, Dark Souls is actually a recent series from 2011. Discounting Other M, the last main line Metroid game came out in 2007. That was Prime 3 with 1.8 million sales according to this site. So maybe gamers might be more interested in giving Metroid a chance thanks to Dark Souls recent success? 

So maybe this time in the industry is perfect for another mainline Metroid like Prime, Super, or Fusion? Or is Metroid forever doomed to sub three million sales? Is Metroid simply a classic IP that is forever niche like Castlevania and Mega Man?

I'm sorry, but neither Metroid, Mega Man or Castlevania is niche games.

I think its fair to call it niche. These game seem to primarily gain their sales from existing fans which continue to decrease generation by generation. And although they reach the million mark and are either genre defining or ranked high in gaming lists, other series with just as high praise like Mario, Zelda (arguably), GTA, Final, Fantasy, and etc make Metroid, Mega Man and Castlevania sales seem miniscule. 

At this point, Nintendo will have to reboot the series in some great way for just make the 2 millions range possible.

A niche game isnt just because of sales. Its about genre, subject matter and overall appeal.

Action platformers with robots, monsters and aliens are not niche.

Niche absolutely means sale. If a game doesn't seem very appealing to the market, then it won't sale as well. Of course sales =/= quality but again sales does show the appeal of games to the market.

And games can have the same genre as other popular game but have very limite sales. Like Xenoblade Chronicles. It's a JRPG and open world. But the game fails to sale over 2 million. That makese Xenoblade Chronicles a niche, too.

If you want to be technical, then you call these game super niche. But the worrying trend about games like Metroid, Castlevania, and Megaman is the fact that these games are bought primarily by their fans which seem to be decreasing each generation. 

It probably stems from the roots of the original game. Metroid was developed by Gunpei Yokoi's development team, unlike Mario and Zelda, developed by Shigeru Miyamoto's team. I'm not sure how the advertising for Metroid was like, but I seriously doubt that it was being pushed as much as Nintendo's larger two flagship titles. I mean, Mario and Zelda had cartoon shows! I'm also not sure if this was Nintendo sticking to safer bets with Miyamoto, or not.

That being said, it's a real shame that Super Metroid sold so little, despite it being a SNES masterpiece.

So every game that sells poorly is a niche game and it has nothing to do with something like marketing or it just being a bad game?

Metroid Prime 1 could easily pass 4 million if it was GC, XBOX, and PS2. I want to say the same for Prime 3 but that had pointer controls.

I honestly don't know what Metroid needs and am fascinated how well Dark Souls is doing. 

Its funny because Nintendo can make a shooter sale well like Splatoon but is still confused on how to market Metroid. I mean just look at how Federation Force was received or why it was even tagged with the Metroid Prime IP in the first place.

Because it's always been too cerebral/solitary/slow of a game. It's beautiful and rewarding but it takes some serious patience on the part of the player to appreciate.

Even the film series that it's inspired by -- Alien never did the type of box office that something like Star Wars does.