I made a quick list of villains (antagonists, jerks, rivals, etc.), that are important and, I believe, are worth to mention:
- Fawful - Mario & Luigi - (Played an important role in two out of four Mario & Luigi games, also appeared in one of the other)
- Waluigi - Wario/Mario - (Very popular)
- King Boo - Luigi's Mansion - (Main antagonist of the Luigi's Mansion series)
- Kamek - Yoshi's Island - (The actual main antagonist of the Yoshi series, often over looked)
- Captain Syrup - Wario (Land) - (Appeared in a lot of Wario Land games. Also played important roles)
- King K. Rool - Donkey Kong - (Obvious)
- Ridley - Metroid - (Also obvious)
- Mother Brain - Metroid - (Important antagonist of the Metroid series)
- Dark Samus - Metroid - (Main antagonist of the Metroid Prime Trilogy)
- Ganon (Wizpig) - The Legend of Zelda - (Actually WAY more important than Sheik)
- Skull Kid - The Legend of Zelda - (Very popular, appeared in quite a few games)
- Ghirahim - The Legend of Zelda - (Very popular)
- Magolor - Kirby - (Very popular)
- Dark Matter - Kirby - (Main antagonist of the "Dark Matter Trilogy")
- Wolf O'Donnell - Star Fox - (Leader of team Star Fox' rivals, team Star Wolf)
- Leon Powalski - Star Fox - (Important member of Team Star Wolf [He is just as important to Star Wolf, as Falco is to Star Fox])
- Andross - Star Fox - (Main antagonist of the Star Fox series)
- Louie - Pikmin - (I know the truth)
- Medusa - Kid Icarus - (Very important to the Kid Icarus series)
- Hades - Kid Icarus - (Main antagonist of Sakurai's favorite game of all time Kid Icarus: Uprising)
- Porky - Mother/Earthbound - (Important [and one of the only] returning character in the Mother/Earthbound series]
- Giygas - Mother/Earthbound - (Important for the Mother/Earthbound series)
- Masked Man - Mother 3 - (Very important character in Mother 3)
- King Hippo - Punch-Out!! - (Not a villain in the traditional way, but a returning and iconic opponent of the Punch-Out!! series)
- Samurai Goro - F-Zero - (Returning character of the F-Zero series, also rival of Captain Falcon)
- Black Shadow - F-Zero - (Important character)
- Meowth - Pokémon - (Iconic and if he gets some Team Rocket references, he technically would count as a villain [etc.], too)
- Dr. Eggman - Sonic - (IF we ever get more than one character per third-party series, I'd prefer him over everyone else from Sonic)
- Dr. Wily - Mega Man - (See above, just replace "Eggman" with "Wily")
I don't know if there are any Fire Emblem or Xenoblade villains that are worth to mention, but I heard Metal Face from Xenobalde is important.
Okay, do you remember when I said "quick"? Yeah, I lied... it is a lot more than I was expecting.
But as you can see, there are actually a lot of important villains (antagonists, etc.). You can't deny, they all are somehow important.
...And this isn't even the tip of the iceberg! I could also have mentioned Panther Caroso from Star Fox, Galacta
Knight from Kirby, Wart from Super Mario Bros. 2, or even the Plasm Wraith from Pikmin 3!
Man, I think I'd kill to have at least the half of them in Smash!
I'm going to rate their chances.
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Fawful -
Mario & Luigi - Only important in the Mario RPG series. Also isn't he dead? Unlikely.
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Waluigi -
Wario/Mario - First of all, not a Wario character. May be popular but not important to the franchise. Unlikely.
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King Boo -
Luigi's Mansion - Very unlikely.
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Kamek -
Yoshi's Island - Very unlikely, but if Yoshi got another rep, it'd be him.
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Captain Syrup -
Wario (Land) - Possible.
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King K. Rool -
Donkey Kong - Duh. VERY LIKELY
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Ridley -
Metroid - Duh. LIKELY WHEN SAKURAI STOPS MAKING SMASH.
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Mother Brain -
Metroid - Can't move and Dinosaur form is literally too big. Unlikely.
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Dark Samus -
Metroid - Possible. Also AT.
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Ganon (Wizpig) -
The Legend of Zelda - Unlikely. Sakurai is set on Falcondorf I guess.
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Skull Kid -
The Legend of Zelda - One time villain. Unlikely. Also AT
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Ghirahim -
The Legend of Zelda - One time villain. Unlikely. Also AT.
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Magolor -
Kirby - To my knowledge, one time villain. Unlikely.
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Dark Matter -
Kirby - Unlikely compared to who he is up against for Smash.
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Wolf O'Donnell -
Star Fox - Duh. Shoo-in
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Leon Powalski -
Star Fox - Unlikely. Leon isn't as important as Falco in the big picture because he's Wolf second hand man, Wolf is the bad guy. Falco is Fox's second hand man, Fox is the good guy. Unlikely.
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Andross -
Star Fox - Is literally just a face and hands, unlikely.
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Louie -
Pikmin - No...
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Medusa -
Kid Icarus - Likely, considering she's important to the series and Sakurai bias.
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Hades -
Kid Icarus - Unlikely compared to Medusa.
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Porky -
Mother/Earthbound - Unlikely, Mother is finished as a franchise (sad I know) and Porky is very wide.
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Giygas -
Mother/Earthbound - Geigue, the feasible form of Giygas in Smash probably won't get in. Unlikely.
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Masked Man -
Mother 3 - Possible
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King Hippo -
Punch-Out!! - Punch Out!! really only needs Little Mac. Unlikely.
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Samurai Goro -
F-Zero - Possible and SHOULD BE IN. Also AT
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Black Shadow -
F-Zero - Important but a lackey to the main villain. Possible.
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Meowth -
Pokémon - Was considered for Smash so likely against the rest of the 716 Pokemon.
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Dr. Eggman -
Sonic - Unlikely, if anyone I'd think it be Tails or Shadow.
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Dr. Wily -
Mega Man - Unlikely, if anyone I'd think it be Protoman or Zero.
Panther Caruso - same reason as Leon unlikely.
Plasm Wraith - Unlikely. One time enemy.
Galacta Knight - Casuals might confuse for Meta Knight and could basically be Meta Knight alt (not saying they are the same) Unlikely.
Wart - One time villain. Unlikely.