Following a sort of unofficial, coincidental trend for this list, today's duo consists of the Gameboy Advance entries, Fusion and Zero Mission. For the purposes of this list, I'm not including the original Metroid (which is freakin' hard, and I don't believe I've ever actually beaten it *gasp*), so ZM counts for both.
Yet again, spoilers abound.
Due to more advanced technology than on the NES, Zero Mission is able to give us a little more interaction on planet Zebes; there are new items to acquire, new enemies and bosses to take down, and perhaps the biggest twist of all, a brand new section of the game that takes place after Mother Brain's demise.
Samus gets shot down after evacuating Zebes, and is forced to infiltrate a Space Pirate mothership in order to regain her lost Power Suit and escape once again. What follows is an intense series of being sneaky and running for your life (those Space Pirates WILL kill you). Once you get all your powers back (including some spiffy new ones), the tides turn and you make quick work of the Space Pirate forces.
As for Fusion, I've explained a bit of the backstory in my SA-X entry a week or so ago, so I'll keep it short. Samus is attacked by a life-form known as an X Parasite, but is saved by a Metroid vaccine. This allows her to absorb the X, which have managed to escape quarantine and run amok on the Biological Space Lab station, killing all staff and most beings onboard. To top it off, an X mimicking Samus at full power is actively searching for her, giving the game quite an ominous atmosphere.
As you progress through the stations various environmental sectors, the X threat increases non-stop. Once you've fought your way through infected creatures and rouge robots and collected much of your lost equipment, you discover a secret lab containing Metroids in all stages of life. The lab ultimately detaches from the station and explodes, but that the Galactic Federation has shown their true colors, Samus is determined to put an end to their plans.
After fighting an X version of Ridley's clone, Samus heads back to the Main Deck to set the station on a collision course with planet SR388, the homeworld of the X Parasites (along the way she passes increasingly larger shed skins). Just before she can access the flight control room, the SA-X shows up for a final showdown and Samus emerges the victor. As she attempts to escape the station, she discovers her ship is missing and is attacked by an Omega Metroid that escaped the secret lab.
Samus is quickly defeated by the far more powerful Metroid, but suddenly the SA-X shows up and begins firing Ice Beam shots (Metroid's one weakness is cold) at the beast. The Omega Metroid kills the SA-X, allowing Samus to absorb it and defeat the creature. She escapes the station, and is now on the run from the Federation.
As I mentioned in the ZM section, I love 2D Metroids (the 3D ones are great too), so these two would naturally be high on the list. Zero Mission gets major points for expanding on an already amazing game (no matter how hard it is), and the post- Mother Brain twist was an unexpected yet pleasant suprise.
However, I feel Fusion is the superior game. I really enjoyed the suspense I felt any time I heard those footsteps (I've already talked about the footsteps...) behind me, and the threat was very much real. I do feel the game was a little strange for telling you where to go, but it's justified in the sense that you usually have to find out how to get there.
Two great games that you owe it to yourself to play! Do it!