When you see the word eigen, replace it with the term spectrum of an operator (see spectral theory) View the matrix as a continuous or discrete linear transform acting on a vector. Similar matrices ($B = MAM^\{-1}$$B = MAM^{-1}$) represent the same transform with respect to a different base.
When you diagonalize the matrix, you are actually trying to obtain an orthogonal decomposition of the transform as a linearly independent eigensystem.
- If there are n independent eigenvectors, you will obtain a full diagonalization of your matrix.
- If less than n, you have two choices. If all eigenvalues are in the ground field, you will get a Jordan decomposition. Otherwise, you have to settle with a rational canonical form.
In addition to Gilbert Strang's excellent book and lectures on Linear Algebra, I recommend browsing through Castillo's Orthogonal sets and polar methods in linear algebra. Throughout the book, the matrix is seen as a transform rather than something which must be numerically manipulated.