Honestly, I always feel that for many publications GOTY often goes to the biggest 'mature' production and not necesarilly the best game. These games tend to be generally widely accepted and publications avoid a plethora of responses like 'Mario iS 4 KiDsz and st00pid' (exaggerating a bit). A lot of it has to do with initial cultural impact and widespread acceptance.
Although they are all good games, I think we'll find that some who apparantly didn't win as many GOTYs eventually wind up as long lasting classics high up on all-time lists. Super Mario Galaxy is for example often named game of the generation despite not wining most GOTY awards.
Metascore, GOTYs.. Personally I tend to judge the true quality of a game in the end by how well it ages, whether that's 2 years later or 10 years later. For me it all depends on how good the underlying core or 'mechanisms' still are (this includes things like level design, controls and story) not so much how impressive the graphics were or how cool this new gimmick was.
Spending warm summer days indoors
Writing frightening verse
To a buck-toothed girl in Luxembourg
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