I can give a couple of reasons. No doubt others can add more.
Firstly, the Newtonian equations of motion are predicated on a Cartesian coordinate system. They do not hold if a non-Cartesian system is used, without a change of form that in many cases makes them unrecognisable. In Lagrangian mechanics the coordinates can be anything at all, eg polar, spherical or a very situation-dependent set of coordinates that reflects system constraints, yet the equations always have the same form.
Secondly, problems are often much easier to solve in Lagrangian form rather than Newtonian. I think the reason is something to do with the fact that Lagrangian is more focused on energy whereas Newtonian is focused on forces and acceleration. For many problems, an energy-based approach is quicker and easier.
Thirdly, they allow uses in electromagnetics where the Lagrangian is not simply an energy-based function and hence, I suspect, not a direct derivation from the Newtonian approach.
I haven't used Hamiltonian approaches much but the impression I get is that one advantage is that they allow an even greater choice of coordinate systems to use. One can choose ##p## ('momentum') coordinates that are not defined as simply ##m\dot{q}##, provided the canonical equations are satisfied.
In my texts Hamiltonian mechanics was introduced principally in order to lay the ground for the standard quantum mechanical formalism, which is built squarely around the Hamiltonian. (although does the Feynman path integral formulation use the Lagrangian? I can't remember).
In a sense the Hamiltonian formulation is more intuitive because the Hamiltonian