In my experience it is often said that the Lagrangian formulation of mechanics can be much much more convenient because the form of the (E-L) equations remains the same whatever coordinates we choose, allowing us to pick as convenience dictates. Often this is exemplified by an example featuring some system constrained to a circle or a sphere, or something.
It is true that the Second Law $\mathbf{F} = m\ddot{\mathbf{x}}$ requires us to express the system in special "inertial" coordinates, but this is fixed easily by introducing a connection and writing $\mathbf{F} = \nabla_{\dot{\mathbf{x}}}\dot{\mathbf{x}}$. Of course, introducing a connection is conceptually identical with declaring certain curves to be geodesics which is conceptually identical with the original speak about "inertial frames." However, it is coordinate-invariant, and as far as I'm concerned coordinate-invariant is coordinate-invariant is coordinate-invariant.