If I understand correctly the connectome would basically be a map of each neuron to its connections, somewhat like a wiring diagram. However, I've heard that it's more realistic to regard each neuron as being more like a computer rather than a wire. Neurons have a lot of state to be accounted for, for example methylated groups controlling the expression of DNA and the resulting amounts and types of various receptors which would influence their control.
For example, some neurons release "neuromodulators" that diffuse beyond their immediate synaptic partners. Electric fields produced by a fiber bundle can affect activity in neighboring neurons.
Inside the cell, there are all kinds of processes on short (millisecond) and long (day) timescales that alter how the same neuron responds to identical stimuli.