2. Remember that Energy is a much fuller concept that those types we "ordinarily" work with, kinetic energy, and those potential energies directly included in the mechanical energy budget balance! The whole of thermodynamics, for example, where energy in the form of heat is included, is one such example.
And, when you therefore work within, for example, a framework and system in which ALL energy is CONSERVED, more advanced variational techniques can be developed here to work as well, but it won't "look like" our ordinary kinematics since those are not the primary variables we work with.
3. In effect, such as Hamiltonian approaches are those that show themselves most amenable to mathematical generalizations, for a vast array of problems, going way beyond "Newtonian" fields of applications.
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Another perspective is the following:
When we are dealing with a complex macro-system, it is in practice IMPOSSIBLE to calculate on a theoretical basis all the subtle effects that go into what we call, say "viscosity", or the local "geometry" of the pipe a fluid, say, flows through.
We use empirically derived APPROXIMATIONS here, and by default, we necessarily have to deal with systems that cannot be given a theoretically "proper" variational/lagrangian formulation (not because it doesn't exist any such, but we're unable to formulate it!). We use Newton by default.
For those particle systems PHYSICISTS look on, what we could call the "core systems of reality", then ALL variables are to be accounted for by means of the truly fundamental laws, and those CAN then be recast in the best apparatus to study them under.