RE 4 doesn't deserve it by any means. A game with so many poor design decisions (no, side step, no quick weapon select, lame inventory system, instant death QTEs, trial and error gameplay, etc) should automatically disqualify it for GOTY.
I'd rather see God of War, Forza, Shadow of the Collossus, Civ IV, Guild Wars, PGR3, Lumines, Mercenaries, or Call of Duty 2 chosen before it.
Sure, give it awards or nominations in Graphics, Art Direction, Sound, and Music but not Design or GOTY.