When I call Mario/Zelda/Metroid the big 3, it's not about sales or recognition. It's about being in a similar space. They're all single-player adventures that originated on the NES and have gone on to have some of Nintendo's best games on most of their systems, particularly the SNES, and to a lesser extent the Gameboy, Gamecube, and Wii. It's a legacy thing more than anything else.
Yep. This is it.
It is also that Metroid is sort of a divergent blend of Mario and Zelda. The pathfinding and gadget puzzles are reminiscent of a Zelda dungeon torn apart and spun out into a maze, but there is also a side-scrolling perspective and a greater focus on platforming.
Mario, Zelda, Metroid span the spectrum of classic Nintendo single-player action-adventure games. I'm more likely to see things like the slew of other Nintendo-platformers in relation to Mario and I'm more likely to see Nintendo's RPGs like Fire Emblem, Mother, or Pokemon as different phenomenona (and less intrinsically "Nintendo," in light of their historical developers and their design philosophies).
For me, Zelda and Metroid form a genre: the Nintendo-style adventure game. Low focus on RPG elements, high focus on 'gadgets' with deeper gameplay altering impact that is played out across puzzles, combat, and traversal. The core differences are a) the gameflow--Zelda has an overworld/underworld dichotomy and works in a more predictable way with you having a series of discrete dungeons; Metroid lacks a discrete overworld and has more irregular progress through the zones, with a mix of focused delves and short forays--and b) Zelda is, in keeping with the above, a less "pure" example: it tends to have side-content in the form of side quests, side dungeons, minigames, town folk, etc.; it also has a stronger tendency towards including RPG mechanics.
You have Metroids closer to the Zelda end of the spectrum: things like Prime 2 or 3, which adopt a Zelda-esque temple structure. You have Zeldas closer to the Metroid end of the spectrum: things like Skyward Sword, which had the dungeons bleed out into the environments surrounding them.
I have a huge problem with this as a lot of the oldschool fans have gone on to shun most things that don't fit that classic mold and scoffed at the newer and quirkier games and only the Marios, the Metroids, the Zeldas get the big spotlight.
I didn't play Metroid until GCN, but SNES was the original formative console for my idea of (console) games. aLttP was my original game. (I have different desires and expectations for PC gaming).
SNES-PSX-PS2/GCN (and GameBoy alongside these) are pretty much where my expectations of games come from. I tend to find classics I go back and play from those eras satisfy me, whereas I find myself out-of-step with both modern triple A and "mobile." (quotes because those games are elsewhere too). I do like puzzle games (which are classics) and I do enjoy some core asepcts of the DS(/GBA) revolution that bled into mobile, like the return of text adventures and the zany minigame collections like WarioWare.
This is a large part of why I tend to go Nintendo/mid-tier Japanese gaming on consoles.
It is a "problem" insofar as it makes me not the consummate modern gamer, but tbh I like my taste as it is for the most part.