Despite multiple nominations, the likes of Call of Duty: Black Ops 2, FIFA 13, Forza Horizon, Halo 4 and Mass Effect 3 did not win a single gong.
I don't know if they were just determined to go against the grain in a couple of the categories.

Dishonoured took the best game award.

Here's the full list, quite a bit of which may well spark some controversy.
Winners in bold and italics.

Debut Game

Deadlight--Raul Rubio, Luz Sancho, Oscar Cuesta
The Unfinished Swan--Ian Dallas, Nathan Gary
Forza Horizon--Development Team
Dear Esther--Daniel Pinchbeck, Robert Briscoe, Jessica Curry
Proteus--Ed Key, David Kanaga
The Room--Development Team

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Original Music

Diablo III--Development Team
Assassin's Creed III--Lorne Balfe
Thomas Was Alone--David Housden
The Unfinished Swan--Joel Corelitz, Keith Leary, Peter Scaturro
Journey--Austin Wintory, Keith Leary, Monty Mudd
The Walking Dead--Jared Emerson-Johnson

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Story

Journey--Development Team
Far Cry 3--Jeffrey Yohalem, Lucien Soulban, Jeffrey Yohalem
The Walking Dead--Development Team
Thomas was Alone--Mike Bithell
Mass Effect 3--Mac Walters
Dishonored--Development Team

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Sports/Fitness

Forza Horizon--Development Team
F1 2012--Development Team
Nike+ Kinect Training--Development Team
New Star Soccer--Simon Read
Trials Evolution--Development Team, Antti llvessup, Kim Lahti
FIFA 13--Development Team

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Game Innovation

Fez--Development Team
Call of Duty: Black Ops II--Development Team
Wonderbook: Books of Spells--Development Team
Journey--Development Team
The Unfinished Swan--Ian Dallas, Nathan Gary, Development Team
Kinect Sesame Street TV--Brian Stone, Josh Atkins, Todd Slepian

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Artistic Achievement

Journey--Development Team
Halo 4--Development Team
Borderlands 2--Randy Pitchford, Paul Hellquist, Jeramy Cooke
Far Cry 3--Jean-Alexis Doyon, Genseki Tanaka, Vincent Jean
The Room--Development Team
Dear Esther--Robert Briscoe

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Online - Browser

The Settlers Online--Christopher Schmitz, Guido Schmidt, Rainer Reber
SongPop--Olivier Michon, Thibaut Crenn, Daouna Jeong
Merlin: The Game--Development Team
Runescape--Development Team
Amateur Surgeon Hospital--Paul Croft, Jim Griffiths
Dick and Dom's Hoopla!--Development Team

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BAFTA Ones To Watch Award

Starcrossed--Kimi Sulopuisto, Vili Viitaniemi, Minttu Meriläinen, Petri Liuska, Andrew MacLean (Kind of a Big Deal)
Project Thanatos--Hugh Laird, Andrew Coles, Thomas Laird, Alexandra Shapland, Thomas Kemp (Raptor Games)
Pixel Story--Martin Cosens, Thomas McParland, Ashley Hayes, Benjamin Rushton, Luke Harrison (Loan Wolf Games)

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Game Design

Dishonored--Development Team
Far Cry 3--Patrick Methè, Jamie Keen
Journey--Development Team
XCOM: Enemy Unknown--Development Team
Borderlands 2--Randy Pitchford, Paul Hellquist, Jeramy Cooke
The Walking Dead--Dan Connors, Kevin Bruner, Kevin Boyle

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Strategy

Dark Souls: Prepare To Die--Development Team
Diablo III--Development Team
Great Big War Game--David Moss, Steve Venezia, Paul Johnson
Total War Shogun 2: Fall of the Samurai--Development Team
Football Manager 2013--Development Team
XCOM: Enemy Unknown--Development Team

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Family

Lego Batman 2: DC Super Heroes--Jon Burton, Jonathan Smith, John Hodskinson
Minecraft: XBOX 360 Edition--Development Team
Just Dance 4--Alkis Argyriadis, Matthew Tomkinson, Veronique Halbrey
Skylanders Giants--Paul Reiche, Fred Ford, Scott Krager
Clay Jam--Chris Roe Iain Gilfeather, Michael Movel
Lego The Lord of the Rings--Jon Burton, James McLoughlin, Nicola Daly

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Audio Achievement

Far Cry 3--Dan Hay, Tony Gronick, Brian Tyler
Beat Sneak Bandit--Simon Flesser, Magnus "Gordon" Gardebäck
Halo 4--Development Team
Assassin's Creed III--Mathieu Jeanson
Dear Esther--Jessica Curry
Journey--Steve Johnson, Austin Wintory, Keith Leary

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Mobile & Handheld

LittleBigPlanet (Vita)--Tom O'Connor, Mattias Nygren, Lee Hutchinson
New Star Soccer--Simon Read
Incoboto--Dene Carter
The Walking Dead--Dan Connors, Kevin Bruner, Kevin Boyle
Super Monsters Ate My Condo--Development Team
The Room--Development Team

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Performer

Nolan North (Nathan Drake)--Uncharted: Golden Abyss
Danny Wallace (The Narrator)--Thomas Was Alone
Melissa Hutchinson (Clementine)--The Walking Dead
Dave Fennoy (Lee Everett)--The Walking Dead
Adrian Hough (Haytham)--Assassin's Creed III
Nigel Carrington (The Narrator)--Dear Esther

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Online - Multiplayer

Assassin's Creed III--Damien Kieken, Mathieu Granjon, Yann Le Guyader
Call of Duty: Black Ops II--Development Team
Journey--Development Team
Need For Speed Most Wanted--Development Team
Halo 4--Development Team
Borderlands 2--Randy Pitchford, Paul Hellquist, Jeramy Cooke

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British Game

Need for Speed Most Wanted--Development Team
Forza Horizon--Development Team
Dear Esther--Daniel Pinchbeck, Robert Briscoe, Jessica Curry
Super Hexagon--Terry Cavanagh, Niamh Houston, Jenn Frank
Lego The Lord of the Rings--Jon Burton, James McLoughlin, Nicola Daly
The Room--Development Team

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Action

Far Cry 3--Dan Hay, Patrick Plourde, Patrik Methe
Hitman: Absolution--Development Team
Call of Duty: Black Ops 2--Development Team
Halo 4--Development Team
Mass Effect 3--Development Team
Borderlands 2--Randy Pitchford, Paul Hellquist, Jeramy Cooke

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Best Game

Far Cry 3--Dan Hay, Patrick Plourde, Patrik Methè
Journey--Development Team
Mass Effect 3--Casey Hudson
Dishonored--Development Team
The Walking Dead--Dan Connors, Kevin Bruner, Kevin Boyle
FIFA 13--Development Team