These are all important caveats, but models of neuron types and connectome change still fit into the overall framework of connectome-based brain simulation. Is there anything about the brain that is fundamentally incompatible with the framework? One difficulty is that neurons can interact outside the confines of synapses. For example, neurotransmitter molecules might escape from one synapse, and diffuse away to be sensed by a more distant neuron. This could lead to interactions between neurons not connected by a synapse, or even between neurons that do not actually contact each other. Because this interaction is extrasynaptic, it is not encompassed in the "wiring diagram;” the connectome. It might be possible to model some extrasynaptic interactions fairly simply. But it's also possible that the diffusion of neurotransmitter molecules in the cramped and tortuous spaces between neurons would require complex models.
If extrasynaptic interactions turn out to be critical for brain function, then it might be necessary to reject the hypothesis "You are your connectome:' The weaker statement "You are your brain" could still be defensible, but this would be much more difficult to use as a basis for uploading [your brain into a computer, as some futurists have proposed]. We might have to throwaway the abstraction of the connectome and descend still further to the atomic level. One could imagine using the laws of physics to create a computer simulation of every atom in a brain. This would be extremely faithful to reality, much more than a connectome-based simulation.
The catch is that a huge number of equations would be necessary, since there are so many atoms. It seems absurd to even consider the enormous computational power required, and is completely out of the question unless your remote descendants survive for galactic time scales. At the present time, it's difficult to simulate even those modest assemblies of atoms called molecules. Simulating all the atoms of a brain is almost beyond imagining. Limited computational power is not the only barrier. There is also the difficulty of obtaining the information to initialize the simulation. It might be necessary to measure all the positions and velocities of the atoms in the brain, which is far more information than in a connectome. It's not clear how to collect that information, or how to do it in a reasonable amount of time.