There is no telling of what might have happened if Newton would have at his disposal some microscopic observations besides the astronomical ones. One thing is sure: the concept of mass would be different today, together with the law of conservation of energy. Therefore the thermodynamics would have also some other form entirely.
However, perhaps one of the most important consequences might have been that of our image of the microscopic world. Such is, for instance, the classical explanation of scattering of alpha particles, which led the scientific community to the planetary image of the atom. Within the framework of Newtonian theory of central forces it does not need a nucleus in order to be explained, but only the possibility of migration of the electric charges in the target metal. Possibly not even that.
Come to think of it: Dewey Larson was right after all! The alpha scattering experiments are indication, not of the nucleus, but of an atomic structure in its entirety. He saw this in the contradictory data on the crystalline lattices and the subsequent dimensions of different atoms deduced from these data. However, this fact can well be a fundamental theoretical one, if we take the central forces as what they are supposed to be, with no strings attached.