Personally I enjoyed Tomb Raider until I had to kill waves of enemies. When I had to pick off 5 or so carefully then I could buy the world they had created. She was young and scared but had been trained to handle weapons and look after herself. As soon as they changed it to "fight x waves of enemies in makehift arenas" then it totally lost me. It became far too Uncharted-clone for it's own good.
So from my point of view I can totally see why they didn't include it in their GOTY but I know the game has it's supporters.
I was going to start a thread asking what the Giantbomb GOTY 2013 will be as this is the first year when I genuinely have no idea. For the last few years it's always been between 2 clear games but this year there doesn't appear to have been a particular standout. I think GTAV or Bioshock Infinite might be the front-runners but Super 3D World could be there, possibly Last of Us if they all play it. There is even an outside chance Gone Home could win it (my personal choice so far).