This for VS11.0.1, but you might try it to see if it works. They indicate to use something like:
vsdiff -t -filespec "*.c *.h" c:\path1 c:\path2
The -t option tells it to recurse subdirectories.
The -filespec option indicates the file types to look for (in this case *.c and *.h).
The other two entities are (obviously) the paths to compare.
HTH,
Dan