Matrix theory is the specialization of linear algebra to the case of finite dimensional vector spaces and doing explicit manipulations after fixing a basis. More precisely: The algebra of $n \times n$ matrices with coefficients in a field $F$ is isomorphic to the algebra of $F$-linear homomorphisms from an $n$-dimensional vector space $V$ over $F$, to itself. And the choice of such an isomorphism is precisely the choice of a basis for $V$.
Sometimes you need concrete computations for which you use the matrix viewpoint. But for conceptual understanding, application to wider contexts and for overall mathematical elegance, the abstract approach of vector spaces and linear transformations is better.
In this second approach you can take over linear algebra to more general settings such as modules over rings(PIDs for instance), functional analysis, homological algebra, representation theory, etc.. All these topics have linear algebra at their heart, or, rather, "is" indeed linear algebra..