Lol. Metroid doesn't have all that many characters.
I have a lot of favorites.
Mother Brain is one. Something about a brain in a tank is awesome. Not to mention how it transforms into a mechanical menace at the end of SM.
Ridley is another one I really like. I love his persistence, and his rivalry with Samus. The roars are all that is necessary to show how much this thing wants to kill Samus. My favorite incarnation is Meta Ridley, I love his return and his dramatic entries. But traditional Ridley is awesome too, I'll never forget when he stole the infant metroid from Ceres Station.
I actually love most or all the bosses in Metroid. I'll list some of my favorites, aside from the above two.
Kraid- I mainly like him for his size. I think Kraid was the first boss to literally tower two screens tall. Correct me if I'm wrong.
Crocomire- I love his design. I like the battle itself too, it was really cool. And the ending *shudder*. I wish he was in Zero Mission.
Phantoon- Ghost. Abandoned ship. Yeah....he was cool....
Chorizo- I liked the concept. The Chozo statues you love and trust are not always what they seem....
Draygon- An awesome boss. I love the grapple trick, where you can literally electrocute him and kill him in one hit. I also liked the mini Draygon's, and I think there were some sea versions in Fusion.....
SA-X- Man I have a love/hate relationship with this thing. It was an all powerful beast that was literally unstoppable.
Metroid Prime/Dark Samus- I like the latter more, mainly because I love doppelgangers. DS had some really cool entrance scenes.
Rundas- He was a really cool character. I liked when he was infested with Phazon, because it really was an emotional scene, something you don't see that much in Metroid. The soundtrack in the battle helped a lot. Ghor was really cool too.
Omega Pirate- Man this thing was crazy. His entrance ranks high on my top boss entrance list.
Quadraxis- Goddamn. What a cool design.
Metroid- Life sucking parasites. Creepy *** things that can literally kill you after they latch onto you.
And of course, I love Samus herself. She was the first female protagonist in any game, unless you count the likes of Ms. PacMan. There is so much mystery behind her, but if you look hard enough, you see she really had a tough upbringing. And who can not like the variety of weapons she has access to.