Not just inductance, but capacitance between the layers themselves too since you've got to have an insulator between them. All the fun things you get in 2d from nanometer scale devices are now compounded in another degree of freedom. The only thing I don't think you have to work around is quantum tunneling between layers because they'll probably be too far apart still to need that level of work.
How thick is "3D" here, and why is that? What makes a bit of vertical distance harder than several mm of horizontal distance?