I’m looking for a beautiful and unifying formalism ...
This is the theory of differential forms on manifolds. An excellent introduction to this is the book by Lee, Smooth Manifolds. If you have come across tensor fields, say in a course on General Relativity, then differential forms are basically alternating covariant tensor fields. It's a different language for the same thing.
that elegantly explains and derives concepts like ... all del operations (gradient, divergence, curl, Laplacian, etc).
To do this precisely requires a metric on the manifold. This is explained in Lee, Riemannian Manifolds. One aspect of this, is that if one forgets about turning covectors into vectors and vice-versa - which is where the metric is used - and focuses solely on covectors, then the natural operator to consider is simply the exterior derivative which transforms a differential form into a closed differential form of one degree higher. Thus in this language grad, curl & div are encoded by the exterior derivative. This applies to any dimension of space. You are not restricted to 3d. In this language the four equations of electromagnetism written in the language of vector analysis turns into two equations of differential forms and this is valid for any dimension of space and for any curved space endowed with a metric.
...are derived in a way that reveals the "shape" of the space we’re working in.
The cohomology of the de Rham complex of differential forms is equivalent to the singular cohomology of the space. Thus it is a topological invariant. This is one way to describe the 'shape' of space.
somthing that can handle these concepts in any coordinate system and provides a clear understanding of the underlying mathematics.
This is the reasoning behind differential geometry on manifolds. The idea is to explore how calculus can be made synthetic (does not rely on coordinates) rather than analytic (does rely on coordinates). The route begins with manifolds which is the coordinate free description of curved space and then differential forms encodes coordinate-free calculus on manifolds.
Another technology is Geometric Algebra. This lifts differential forms to calculus with Clifford algebras. In this language, the four equations of electromagnetism reduces to one equation of geometric algebra.