Disproportion in cranial nerve innervation?
We can somewhat rule out reason 1 because fingertips are also highly sensitive to sensory stimulus. Moreover innervation is not solely about sensory inputs but also motor functions, visceral control etc. All the nerves required for the motor function and a significant portion of visceral control nerves connect to spinal cord.

Therefore in my opinion reason 2 is the most appropriate which automatically rules out reason 3. 
Spinal cord is an advancement of neural organization in the chordates. Spinal cord can be viewed as a central cable in which all power lines merge (they still maintain their individuality [the spinal tracts]; they just get clustered to form an organized bundle). Evolution of spinal reflexes must have been a secondary event. 

The case of vagus nerve and cranioaccessory nerve suggests that this is an ancient pathway to control the heart. Heart with a closed circulatory system is found in molluscs as well. Apart from the functional significance of the heart (which might to some extent justify direct cranial innervation), it is decently proximal to the brain as well.