Protagonists (in no particular order, save for the number 1):

• Francis York Morgan (Deadly Premonition)
  
• Geralt (The Witcher)
  
• Guybrush Threepwood (Monkey Island series)
  
• Warlord Gorgutz 'Eadhunta (Dawn of War: Winter Assault and Dark Crusade)
  
• Eldred (Sacrifice)
  
• Banjo & Kazooie (Banjo and Kazooie games)
  
• Kratos (God of War series)
  
• Professor Layton (Professor Layton series)
  
• The Saints Row Gang Leader (Saints Row 2)
  
• Amaterasu (Okami)

Antagonists (in no particular order):

• President Eden (Fallout 3)
  
• Mithras/Marduke (Sacrifice)
  
• Lavos (Chrono Trigger)
  
• Ocelot (Metal Gear Solid 1, 2, 3, and 4)
  
• Gannondorf (Ocarina of Time, Windwaker, and Twilight Princess)
  
• Andrew Ryan (Bioshock)
  
• Kefka Palazoo (Final Fantasy VI)
  
• GLaDOS (Portal)
  
• Baal (Diablo II and Lord of Destruction)
  
• Majora (LoZ: Majora's Mask)
  
• Dagoth Ur (The Elder Scrolls III: Morrowind)

It was bad, but the fanservicy'est thing was easily Miranda. Yes Tali's romance made her character change and pretty much retconned (or atleast downplayed how terrible quarians immune systems are) the quarians immune problems. But Miranda for no reason had a skintight suit, and the camera showed her ass more than her face.

Also Ashley got ruined by fanservice, she now has heels, tighter armour and long hair...

In order from favored to least favored.


Pro:
Link Legend Of Zelda
Chell Portal
Banjo and Kazooie Banjo and Kazooie
Sonic Sonic The Hedgehog
Mario SUPER MARIO BROS
Donkey Kong Donkey Kong

Ant
Glados Portal
Ganondorf Legend Of Zelda
Bowser Super Mario

Something like this, in no particular order:

Protagonist

Zidane Tribal - Final Fantasy IX
Squall Leonhart - Final Fantasy VIII
Auron - Final Fantasy X
Aqua - Kingdom Hearts: Birth by Sleep
Sora - Kingdom Hearts
Samus Aran - Metroid
Solid Snake - Metal Gear Solid
Mega Man Volnutt - Mega Man Legends
Mitsuru Kirijo - Persona 3
Amaterasu - Okami

Antagonist

Kuja - Final Fantasy IX
Ultimecia - Final Fanasy VIII
Zemus - Final Fantasy IV
Master Xehanort - Kingdom Hearts: Birth by Sleep
Sovereign - Mass Effect
Sigma - Mega Man X
Ganondorf - The Legend of Zelda
Revolver Ocelot - Metal Gear Solid
Lavos - Chrono Trigger
Selvaria Bles - Valkyria Chronicles

I'm sure I'm missing some big ones though.

You're right of course, but the difference is, Miranda didn't really get ruined for fanservice, she just started out as Ms. Fanservice. Tali's character was already there, and because so many nerds turned her into their Ideal Woman (with chicken feet?), BioWare decided to give the nerds a break and completely alter Tali's character to make her romanceable. The very thing that made Tali's character so interesting, however, was the complete lack of sixual or romantic tension - where Ashley/Kaidan/Liara was the love interest, Tali was the character you could just talk to and like, without all the romance crap. But no, they just HAD to make her romanceable, no matter how illogical. As for Ashley, I don't watch trailers or previews to have a completely spoiler-free experience, but I don't think it'd be that bad to have her appear a little more feminine.

He's still an antagonist for part of the game, though. I'd compare him to

"Antagonist" doesn't really have to mean "evil". All an antagonist is, by its definition, is a character who works against the main character at some point.