The series' tonal shift from serious to comedy/serious/camp. For me, its truly spoiled the show.
Dean's voice: Ackles doesn't have a gruff voice. So its annoying hearing it, especially when Dean's voice wasn't presented that way from the very beginning.
The loss of the Yellow Eyed Demon & Sam's powers.
The introduction of religious deities (Angels, God, Devil, etc) doesn't mesh well with mythical or urban creatures, nor the series title of 'Supernatural'.