For a SISO (single input single output) LTI (linear time invariant) system, there is a well defined notion of dual representations of the system. This duality is delt with in this question. To briefly summarize, a rational transfer matrix $\mathbf{G}(s)$ for the system $\hat{\mathbf{y}}(s) = \mathbf{G}(s) \hat{\mathbf{u}}(s)$ can be represented by the system $$\frac{d \mathbf{x}}{dt} = \mathbf{A}\mathbf{x} + \mathbf{B} \mathbf{u} \qquad \mathbf{y} = \mathbf{C}\mathbf{x}+\mathbf{D}\mathbf{u}$$ when $\mathbf{G}(s) = \mathbf{C}(s\mathbf{I}-\mathbf{A})^{-1}\mathbf{B} + \mathbf{D}$; here I use a hat to denote Laplace transform. For a SISO system, $\mathbf{u}$, $\mathbf{y}$, and $\mathbf{G}$ are scalars, and thus the transfer function $\mathbf{G}$ is equal to its transpose, $$\mathbf{G}(s) = \mathbf{G}(s)^T = \mathbf{B}^T(s\mathbf{I}-\mathbf{A}^T)^{-1}\mathbf{C}^T + \mathbf{D}^T$$ and thus the systems $(\mathbf{A},\mathbf{B},\mathbf{C},\mathbf{D})$ and $(\mathbf{A}^T,\mathbf{C}^T,\mathbf{B}^T,\mathbf{D}^T)$ are representations of the same transfer function, and the latter is termed the dual of the former.
For a MIMO (multi input multi output) system, the transfer matrix is not necessarily equal to its transpose, and thus the dual of a system, while it can be defined, is fundamentally a different system.
What is the connection between a system and its dual for the MIMO case?
I appreciate that taking the dual of the system swaps the controllability and observability properties, and that is why it is used. However, I have no intuitive understanding of what this mathematical trick is doing. I would expect the dual to be related to an inner product: the transpose is the adjoint operator for a matrix and thus $\langle \hat{\mathbf{w}},\mathbf{G} \hat{\mathbf{u}} \rangle = \langle \bar{\mathbf{G}}^T\hat{\mathbf{w}}, \hat{\mathbf{u}} \rangle$ for any $\hat{\mathbf{w}}(s)$. I can't seem to use this to construct the dual system, nor use it to motivate a connection between the controllability and observability of the resulting systems.