Doctor WHo: The Pandorica OPENS!
re: I wonder Who the major villain is.
couple of questions unresolved of course (note the Capitalizations): Who is/was controlling the Tardis remotely? Who really caused the cracks in the universe? Who caused the feedback through the monitor as River was trying to land the Tardis in The Pandorica Opens which caused a feedback first audibly and then took over the screen and said in an older, more sinister voice "Silence will fall!" .. I earnestly HOPE it is the VALEYARD! ...for those of you not knowing, or not have read my previous post on this, the Valeyard is "an amalgamation of the darker sides of the Doctor, somewhere between his 12th and final regenerations." as seen from the Colin Baker season "Trial of a Timelord".
The Valeyard IS The Doctor. The Valeyard can easily explain all that is going on with the cracks, the Pandorica, etc.