As far as Metroid, Super Metroid has got to be the best 2D, but let me explain why. It is mainly a more balanced, and generally improved version of the first game. I love the music, and sense of freedom, and exploration.
Some exploration aspects seem to have been lost in Metroid 1's transition into Zero Mission. The game was more "go here, then there, and this statue will show you". It was still awesome though, and I liked the Chozodia, and Space Pirate Ship areas.
Fusion was cool, but it took away a lot of the immediate exploration and replaced it with missions. You couldn't really go and explore until about mid-way through the game. Metroid 2 was okay, in the same sense that Zelda 2 was, and the original SMB2 was. It was interesting to say the least, but it seems that the second game of any main Nintendo franchise can be compared to those awkward teenage years when you try and find a medium somewhere between childhood, and adulthood.. Eh.
Now, Prime was awesome. It would let you explore, and giver you hints if you wandered around an enough. This encouraged exploration, and got rid of simply getting lost. In fact, Prime 1 was the only Prime game where you could truly get lost. Prime 2 sucks flat out. Ammo, and a stupid-ass dark world? No thanks. Gimme unlimited awesome beams, and a game that doesn't spend half of its time in same lame ass bubble hoping dark world with annoying enemies. Prime 2 DID have and awesome 'red' Brinstar remix though. That is one redeeming quality.
Prime 3 was okay, but felt too mainstream, and seemed to lose a lot of Metroid. Voice acting, several characters, and a fleet of ships and going form planet to planet? Not necessarily bad, but it didn't feel Metroid. Level design focused too much on backgrounds, and not as much on exploration. Sure, we can see these awesome panoramas, but we can't actually go there.
I'm done for now.
EDIT:
russadwan wrote:I have to disagree there.Especially since the bosses are invisible when I try to play it on my DS. Last night I had to fiddle with the graphical settings for an hour before I could even see Kraid.
That, good sir, is your own fault for pirating it, and you can't blame the hardware if it is an illegal version/means of playing. I'm not against ROMs, I'm just sayin' you can't complain unless you are playing it the way it is meant to be played :]